Release Notes For GenBank Release 131

GBREL.TXT          Genetic Sequence Data Bank
                         August 15 2002

               NCBI-GenBank Flat File Release 131.0

                    Distribution Release Notes

 18197119 loci, 22616937182 bases, from 18197119 reported sequences

  This document describes the format and content of the flat files that
comprise releases of the GenBank database. If you have any questions or
comments about GenBank or this document, please contact NCBI via email
at info@ncbi.nlm.nih.gov or:

   GenBank
   National Center for Biotechnology Information
   National Library of Medicine, 38A, 8N805
   8600 Rockville Pike
   Bethesda, MD  20894
   USA
   Phone:  (301) 496-2475
   Fax:    (301) 480-9241

==========================================================================
TABLE OF CONTENTS
==========================================================================

1. INTRODUCTION

1.1 Release 131.0
1.2 Cutoff Date
1.3 Important Changes in Release 131.0
1.4 Upcoming Changes
1.5 Request for Direct Submission of Sequence Data
1.6 Organization of This Document

2. ORGANIZATION OF DATA FILES

2.1 Overview
2.2 Files
     2.2.1 File Descriptions
     2.2.5 File Sizes
     2.2.6 Per-Division Statistics 
     2.2.7 Selected Per-Organism Statistics 
     2.2.8 Growth of GenBank

3. FILE FORMATS

3.1 File Header Information
3.2 Directory Files
     3.2.1 Short Directory File
3.3 Index Files
     3.3.1 Accession Number Index File
     3.3.2 Keyword Phrase Index File
     3.3.3 Author Name Index File
     3.3.4 Journal Citation Index File
     3.3.5 Gene Name Index
3.4 Sequence Entry Files
     3.4.1 File Organization
     3.4.2  Entry Organization
     3.4.3 Sample Sequence Data File
     3.4.4 LOCUS Format
     3.4.5 DEFINITION Format
          3.4.5.1 DEFINITION Format for NLM Entries
     3.4.6 ACCESSION Format
     3.4.7 VERSION Format
     3.4.8 KEYWORDS Format
     3.4.9 SEGMENT Format
     3.4.10 SOURCE Format
     3.4.11 REFERENCE Format
     3.4.12 FEATURES Format
          3.4.12.1 Feature Key Names
          3.4.12.2 Feature Location
          3.4.12.3  Feature Qualifiers
          3.4.12.4 Cross-Reference Information
          3.4.12.5 Feature Table Examples
     3.4.13 ORIGIN Format
     3.4.14 SEQUENCE Format

4. ALTERNATE RELEASES

5. KNOWN PROBLEMS OF THE GENBANK DATABASE

5.1 Incorrect Gene Symbols in Entries and Index

6. GENBANK ADMINISTRATION 

6.1 Registered Trademark Notice
6.2 Citing GenBank
6.3 GenBank Distribution Formats and Media
6.4 Other Methods of Accessing GenBank Data
6.5 Request for Corrections and Comments
6.6 Credits and Acknowledgments
6.7 Disclaimer

==========================================================================

1. INTRODUCTION

1.1 Release 131.0

  The National Center for Biotechnology Information (NCBI) at the National
Library of Medicine (NLM), National Institutes of Health (NIH) is responsible
for producing and distributing the GenBank Sequence Database.  NCBI handles
all GenBank direct submissions and authors are advised to use the address
below.  Submitters are encouraged to use the free Sequin software package
for sending sequence data, or the newly developed World Wide Web submission
form.  See Section 1.5 below for details.

*****************************************************************************

The address for direct submissions to GenBank is:

       GenBank Submissions
       National Center for Biotechnology Information
       Bldg 38A, Rm. 8N-803
       8600 Rockville Pike
       Bethesda, MD 20894

       E-MAIL:  gb-sub@ncbi.nlm.nih.gov

Updates and changes to existing GenBank records:

       E-MAIL:  update@ncbi.nlm.nih.gov

URL for the new GenBank submission tool - BankIt - on the World Wide Web:

       http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/

(see Section 1.5 for additional details about submitting data to GenBank.)

*****************************************************************************

  GenBank Release 131.0 is a release of sequence data by NCBI in the GenBank
flatfile format.  GenBank is a component of a tri-partite, international
collaboration of sequence databases in the U.S., Europe, and Japan.  The
collaborating databases in Europe are the European Molecular Biology Laboratory
(EMBL) at Hinxton Hall, UK, and the DNA Database of Japan (DDBJ) in Mishima,
Japan. Sequence data is also incorporated from the Genome Sequence Data Base
(GSDB), Santa Fe, NM.  Patent sequences are incorporated through arrangements
with the U.S. Patent and Trademark Office, and via the collaborating
international databases from other international patent offices.  The database
is converted to various output formats, including the Flat File and Abstract
Syntax Notation 1 (ASN.1) versions.  The ASN.1 and Flat File forms of the data
are available at NCBI's anonymous FTP server: ftp.ncbi.nih.gov .

1.2 Cutoff Date

  This full release, 131.0, incorporates data available to the collaborating
databases as of August 23, 2002.  For more recent data, users are advised to:

  o Download the GenBank Update files by anonymous FTP to 'ftp.ncbi.nih.gov':

	ftp://ftp.ncbi.nih.gov/ncbi-asn1 (ASN.1 format)
	ftp://ftp.ncbi.nih.gov/genbank   (flatfile format)

    Mirrors of the GenBank FTP site at the NCBI are available from the San Diego
    Supercomputer Center and the University of Indiana:

	ftp://genbank.sdsc.edu/pub
	ftp://bio-mirror.net/biomirror/genbank/

    Some users who experience slow FTP transfers of large files (entire releases,
    the GenBank Cumulative Update, etc) might realize an improvement in transfer
    rates from these alternate sites when traffic at the NCBI is high.

  o Use the interactive Network-Entrez or Web-Entrez applications to query
    the 'Entrez: Nucleotides' database (see Section 6.4 of this document).

1.3 Important Changes in Release 131.0

1.3.1 Organizational changes

  Due to database growth, the EST division is now being split into 178 pieces.

  Due to database growth, the GSS division is now being split into 52 pieces.

  Due to database growth, the HTG division is now being split into 43 pieces.

  Due to database growth, the PRI division is now being split into 22 pieces.

  Due to database growth, the ROD division is now being split into 4 pieces.

1.3.2 GSS File Header Problem

  GSS sequences at GenBank are maintained in one of two different systems,
depending on their origin. One recent change to release processing involves
the parallelization of the dumps from those systems. Because the second dump
(for example) has no prior knowledge of exactly how many GSS files will be
dumped from the first, it doesn't know how to number it's own output files.
There is thus a discrepancy between the filenames and file headers of eight
GSS flatfiles in Release 131.0. Consider the gbgss45.seq file:

GBGSS1.SEQ           Genetic Sequence Data Bank
                           August 15 2002

                NCBI-GenBank Flat File Release 131.0

                           GSS Sequences (Part 1)

  Here, the filename and part number in the header is "1", though the file
has been renamed as "45" based on the files dumped from the other system.
We will work to resolve this discrepancy in future releases, but the priority
is admittedly much lower than many other tasks.

1.3.3 Selenocysteine representation

  At the May 1999 DDBJ/EMBL/GenBank collaborative meeting, it was learned
that IUPAC plans to adopt the letter 'U' for selenocysteine.

  With this August 2002 release, selenocysteine residues are now presented
via residue abbreviation 'U', in both /translation and /transl_except
qualifiers.

1.4 Upcoming Changes

1.4.1 Change to the SOURCE and ORGANISM format

The GenBank flatfile format utilizes two different formats for the SOURCE
linetype, depending on the existence of a designated common name in the
GenBank Taxonomy Database -

   --- Current GenBank format ---

SOURCE    [organism name] OR [common name]
ORGANISM  [organelle prefix] organism name

Starting with GenBank release 132.0 in October 2002, a new more flexible
SOURCE format will be adopted, allowing for the display of several types
of secondary names (common names, acronyms, synonyms, anamorphs for the fungi)
which can be derived either from the taxonomy database *or* from the source
feature annotation provided by the submitter.

In addition, the optional organelle prefix will move from the ORGANISM line 
(in the old format) to the SOURCE line in the new format. The ORGANISM line
will contain only the unadorned organism name, the name by which a sequence
entry is indexed in the taxonomy database.

   --- NEW GenBank format ---

SOURCE    [organelle prefix] organism name ([optional second name])
ORGANISM  organism name

The optional second name can be one of the following (ordered by precedence) -

  'synonym' from the source feature organism modifiers (submitter-supplied)
  'acronym' from the source feature organism modifiers (submitter-supplied)
  'anamorph' from the source feature organism modifiers (submitter-supplied)
  'common' from the source feature organism modifiers (submitter-supplied)

  'genbank synonym' from the taxonomy database
  'genbank acronmym' from the taxonomy database
  'genbank anamorph' from the taxonomy database
  'genbank common name' from the taxonomy database

The first set allows us to customize the flatfiles of particular entries,
the last allow us to add useful & informative information from the
taxonomy database (with a more reasonable presentation than in the
current flatfiles).

The 'anamorph' names will appear within parentheses prefixed with
(anamorph: ---). The 'common name', 'acronym' and 'synonym' fields will be 
parenthesized without a prefix (see examples below).

The SOURCE line organelle prefix will correspond to the most detailed portion
of the string value for the /organelle qualifier of the source feature. This
allows us to annotate everything with the correct general terms, yet prominently
display the familiar 'Chloroplast' & 'Kinetoplast' :

  organelle qualifer            SOURCE organelle prefix
  -----------------             -----------------------
  "plastid"                     plastid
  "mitochondrion"               mitochondrion
  "nucleomorph"                 nucleomorph
  "mitochondrion: kinetoplast"  kinetoplast
  "plastid: chloroplast"        chloroplast
  "plastid: apicoplast"         apicoplast
  "plastid: chromoplast"        chromoplast
  "plastid: cyanelle"           cyanelle
  "plastid: leucoplast"         leucoplast
  "plastid: protoplast"         protoplast

=======================================================
======          Examples of the new format       ======
=======================================================

In all of the examples below, the source feature qualifiers given
in the first part of the example will automatically generate the
SOURCE & ORGANISM lines shown:

------------------------

  /organism="Sus scrofa"

SOURCE      Sus scrofa (pig)
ORGANISM    Sus scrofa

'pig' is the genbank common name from the GenBank taxonomy database.

------------------------

  /organism="Sus scrofa"
  /note="common: Japanese wild boar"

SOURCE      Sus scrofa (Japanese wild boar)
ORGANISM    Sus scrofa

The common name from the source feature (submittor-suppllied) for
the entry overrides the common name from the GenBank taxonomy database
with the new SOURCE format.

------------------------

  /organism="Takifugu rubripes"

SOURCE       Takifugu rubripes (Fugu rubripes)
ORGANISM     Takifugu rubripes

'genbank synonym' from the taxonomy database is displayed on the SOURCE
line.

------------------------

  /organism="Takifugu rubripes"
  /note="common: Sydney's pufferfish"

SOURCE       Takifugu rubripes (Sydney's pufferfish)
ORGANISM     Takifugu rubripes

Any of the customizing fields from the entry itself take precedence
over the default values from the taxonomy database.

------------------------

  /organism="Cauliflower mosaic virus"

SOURCE       Cauliflower mosaic virus (CaMV)
ORGANISM     Cauliflower mosaic virus

If there is a single acronym listed in the taxonomy database,
it will appear on the SOURCE line.

------------------------

'genbank anamorph' (from the taxonomy database) 

  /organism="Emericella nidulans"

SOURCE       Emericella nidulans (anamorph: Aspergillus nidulans)
ORGANISM     Emericella nidulans

The 'anamorph' nametype is prefixed with "anamorph:" on the SOURCE line
to distinguish it from a taxonomic synonym.

------------------------

  /organism="Mytilus californicus"
  /organelle="mitochondrion"

SOURCE       mitochondrion Mytilus californicus (California mussel)
ORGANISM     Mytilus californicus

Organelle prefix moved to SOURCE, with common name from the
GenBank taxonomy database.

Additional information about this change will be presented via the
GenBank release notes, and via the GenBank newsgroup.

1.5 Request for Direct Submission of Sequence Data

  A successful GenBank requires that sequence data enter the database as
soon as possible after publication, that the annotations be as complete as
possible, and that the sequence and annotation data be accurate. All
three of these requirements are best met if authors of sequence data
submit their data directly to GenBank in a usable form. It is especially
important that these submissions be in computer-readable form.

  GenBank must rely on direct author submission of data to ensure that
it achieves its goals of completeness, accuracy, and timeliness. To
assist researchers in entering their own sequence data, GenBank
provides a WWW submission tool called BankIt, as well as a stand-alone
software package called Sequin. BankIt and Sequin are both easy-to-use
programs that enable authors to enter a sequence, annotate it, and
submit it to GenBank.  Through the international collaboration of DNA
sequence databases, GenBank submissions are forwarded daily for inclusion
in the EMBL and DDBJ databases.

  SEQUIN.  Sequin is an interactive, graphically-oriented program based
on screen forms and controlled vocabularies that guides you through the
process of entering your sequence and providing biological and
bibliographic annotation.  Sequin is designed to simplify the sequence submission
process, and to provide increased data handling capabilities to accomodate
very long sequences, complex annotations, and robust error checking.  E-mail
the completed submission file to : gb-sub@ncbi.nlm.nih.gov

  Sequin is provided for Macintosh, PC/Windows, UNIX and VMS computers.
It is available by annonymous ftp from ftp.ncbi.nih.gov; login as
anonymous and use your e-mail address as the password. It is located in
the sequin directory. Or direct your web browser to this URL:

	ftp://ftp.ncbi.nih.gov/sequin

  BANKIT.  BankIt provides a simple forms approach for submitting your
sequence and descriptive information to GenBank.  Your submission will
be submitted directly to GenBank via the World Wide Web, and
immediately forwarded for inclusion in the EMBL and DDBJ databases.
BankIt may be used with Netscape, Internet Explorer, and other common
WWW clients. You can access BankIt from GenBank's home page:   

	http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/

  AUTHORIN.  Authorin sequence submissions are no longer accepted by
GenBank, and the Authorin application is no longer distributed by NCBI.  

  If you have questions about GenBank submissions or any of the data
submission tools, contact NCBI at: info@ncbi.nlm.nih.gov or 301-496-2475.

1.6 Organization of This Document

  The second section describes the contents of GenBank releases. The third
section illustrates the formats of the flat files.  The fourth section
describes other versions of the data, the fifth section identifies known prob-
lems, and the sixth contains administrative details.

2. ORGANIZATION OF DATA FILES

2.1 Overview

  GenBank releases consist of a set of ASCII text files, most of which
contain sequence data. A few supplemental "index" files are also supplied,
containing comprehensive lists of author names, journal citations,
gene names, and keywords, along with the accession numbers of the records
in which they can be found (see Section 3.3). The line-lengths of
these files is variable.

2.2 Files

  This GenBank flat file release consists of 351 files. The lists
that follow describe each of the files included in the distribution.
Their sizes and base pair content are also summarized.

2.2.1 File Descriptions

1.  gbrel.txt	- Release notes (this document).
2.  gbsdr.txt 	- Short directory of the data bank.
3.  gbacc.idx 	- Index of the entries according to accession number.
4.  gbkey.idx 	- Index of the entries according to keyword phrase.
5.  gbaut1.idx 	- Index of the entries according to author, part 1.
6.  gbaut2.idx 	- Index of the entries according to author, part 2.
7.  gbaut3.idx 	- Index of the entries according to author, part 3.
8.  gbaut4.idx 	- Index of the entries according to author, part 4.
9.  gbaut5.idx 	- Index of the entries according to author, part 5.
10. gbaut6.idx 	- Index of the entries according to author, part 6.
11. gbaut7.idx 	- Index of the entries according to author, part 7.
12. gbaut8.idx 	- Index of the entries according to author, part 8.
13. gbaut9.idx 	- Index of the entries according to author, part 9.
14. gbaut10.idx - Index of the entries according to author, part 10.
15. gbaut11.idx - Index of the entries according to author, part 11.
16. gbaut12.idx - Index of the entries according to author, part 12.
17. gbjou.idx 	- Index of the entries according to journal citation.
18. gbgen.idx 	- Index of the entries according to gene names.
19. gbsec.idx	- Index of the entries according to secondary accession number.
20. gbpri1.seq 	- Primate sequence entries, part 1.
21. gbpri2.seq 	- Primate sequence entries, part 2.
22. gbpri3.seq 	- Primate sequence entries, part 3.
23. gbpri4.seq 	- Primate sequence entries, part 4.
24. gbpri5.seq 	- Primate sequence entries, part 5.
25. gbpri6.seq 	- Primate sequence entries, part 6.
26. gbpri7.seq 	- Primate sequence entries, part 7.
27. gbpri8.seq 	- Primate sequence entries, part 8.
28. gbpri9.seq 	- Primate sequence entries, part 9.
29. gbpri10.seq	- Primate sequence entries, part 10.
30. gbpri11.seq	- Primate sequence entries, part 11.
31. gbpri12.seq	- Primate sequence entries, part 12.
32. gbpri13.seq	- Primate sequence entries, part 13.
33. gbpri14.seq	- Primate sequence entries, part 14.
34. gbpri15.seq	- Primate sequence entries, part 15.
35. gbpri16.seq	- Primate sequence entries, part 16.
36. gbpri17.seq	- Primate sequence entries, part 17.
37. gbpri18.seq	- Primate sequence entries, part 18.
38. gbpri19.seq	- Primate sequence entries, part 19.
39. gbpri20.seq	- Primate sequence entries, part 20.
40. gbpri21.seq	- Primate sequence entries, part 21.
41. gbpri22.seq	- Primate sequence entries, part 22.
42. gbrod1.seq 	- Rodent sequence entries, part 1.
43. gbrod2.seq 	- Rodent sequence entries, part 2.
44. gbrod3.seq 	- Rodent sequence entries, part 3.
45. gbrod4.seq 	- Rodent sequence entries, part 4.
46. gbmam.seq 	- Other mammalian sequence entries.
47. gbvrt1.seq 	- Other vertebrate sequence entries, part 1.
48. gbvrt2.seq 	- Other vertebrate sequence entries, part 2.
49. gbinv1.seq 	- Invertebrate sequence entries, part 1.
50. gbinv2.seq 	- Invertebrate sequence entries, part 2.
51. gbinv3.seq 	- Invertebrate sequence entries, part 3.
52. gbinv4.seq 	- Invertebrate sequence entries, part 4.
53. gbinv5.seq 	- Invertebrate sequence entries, part 5.
54. gbpln1.seq 	- Plant sequence entries (including fungi and algae), part 1.
55. gbpln2.seq 	- Plant sequence entries (including fungi and algae), part 2.
56. gbpln3.seq 	- Plant sequence entries (including fungi and algae), part 3.
57. gbpln4.seq 	- Plant sequence entries (including fungi and algae), part 4.
58. gbpln5.seq 	- Plant sequence entries (including fungi and algae), part 5.
59. gbpln6.seq 	- Plant sequence entries (including fungi and algae), part 6.
60. gbbct1.seq 	- Bacterial sequence entries, part 1.
61. gbbct2.seq 	- Bacterial sequence entries, part 2.
62. gbbct3.seq 	- Bacterial sequence entries, part 3.
63. gbbct4.seq 	- Bacterial sequence entries, part 4.
64. gbbct5.seq 	- Bacterial sequence entries, part 5.
65. gbvrl1.seq 	- Viral sequence entries, part 1.
66. gbvrl2.seq 	- Viral sequence entries, part 2.
67. gbvrl3.seq 	- Viral sequence entries, part 3.
68. gbphg.seq 	- Phage sequence entries.
69. gbsyn.seq 	- Synthetic and chimeric sequence entries.
70. gbuna.seq 	- Unannotated sequence entries.
71. gbest1.seq  - EST (expressed sequence tag) sequence entries, part 1.
72. gbest2.seq  - EST (expressed sequence tag) sequence entries, part 2.
73. gbest3.seq  - EST (expressed sequence tag) sequence entries, part 3.
74. gbest4.seq  - EST (expressed sequence tag) sequence entries, part 4.
75. gbest5.seq  - EST (expressed sequence tag) sequence entries, part 5.
76. gbest6.seq  - EST (expressed sequence tag) sequence entries, part 6.
77. gbest7.seq  - EST (expressed sequence tag) sequence entries, part 7.
78. gbest8.seq  - EST (expressed sequence tag) sequence entries, part 8.
79. gbest9.seq  - EST (expressed sequence tag) sequence entries, part 9.
80. gbest10.seq - EST (expressed sequence tag) sequence entries, part 10.
81. gbest11.seq - EST (expressed sequence tag) sequence entries, part 11.
82. gbest12.seq - EST (expressed sequence tag) sequence entries, part 12.
83. gbest13.seq - EST (expressed sequence tag) sequence entries, part 13.
84. gbest14.seq - EST (expressed sequence tag) sequence entries, part 14.
85. gbest15.seq - EST (expressed sequence tag) sequence entries, part 15.
86. gbest16.seq - EST (expressed sequence tag) sequence entries, part 16.
87. gbest17.seq - EST (expressed sequence tag) sequence entries, part 17.
88. gbest18.seq - EST (expressed sequence tag) sequence entries, part 18.
89. gbest19.seq - EST (expressed sequence tag) sequence entries, part 19.
90. gbest20.seq - EST (expressed sequence tag) sequence entries, part 20.
91. gbest21.seq - EST (expressed sequence tag) sequence entries, part 21.
92. gbest22.seq - EST (expressed sequence tag) sequence entries, part 22.
93. gbest23.seq - EST (expressed sequence tag) sequence entries, part 23.
94. gbest24.seq - EST (expressed sequence tag) sequence entries, part 24.
95. gbest25.seq - EST (expressed sequence tag) sequence entries, part 25.
96. gbest26.seq - EST (expressed sequence tag) sequence entries, part 26.
97. gbest27.seq - EST (expressed sequence tag) sequence entries, part 27.
98. gbest28.seq - EST (expressed sequence tag) sequence entries, part 28.
99. gbest29.seq - EST (expressed sequence tag) sequence entries, part 29.
100. gbest30.seq - EST (expressed sequence tag) sequence entries, part 30.
101. gbest31.seq - EST (expressed sequence tag) sequence entries, part 31.
102. gbest32.seq - EST (expressed sequence tag) sequence entries, part 32.
103. gbest33.seq - EST (expressed sequence tag) sequence entries, part 33.
104. gbest34.seq - EST (expressed sequence tag) sequence entries, part 34.
105. gbest35.seq - EST (expressed sequence tag) sequence entries, part 35.
106. gbest36.seq - EST (expressed sequence tag) sequence entries, part 36.
107. gbest37.seq - EST (expressed sequence tag) sequence entries, part 37.
108. gbest38.seq - EST (expressed sequence tag) sequence entries, part 38.
109. gbest39.seq - EST (expressed sequence tag) sequence entries, part 39.
110. gbest40.seq - EST (expressed sequence tag) sequence entries, part 40.
111. gbest41.seq - EST (expressed sequence tag) sequence entries, part 41.
112. gbest42.seq - EST (expressed sequence tag) sequence entries, part 42.
113. gbest43.seq - EST (expressed sequence tag) sequence entries, part 43.
114. gbest44.seq - EST (expressed sequence tag) sequence entries, part 44.
115. gbest45.seq - EST (expressed sequence tag) sequence entries, part 45.
116. gbest46.seq - EST (expressed sequence tag) sequence entries, part 46.
117. gbest47.seq - EST (expressed sequence tag) sequence entries, part 47.
118. gbest48.seq - EST (expressed sequence tag) sequence entries, part 48.
119. gbest49.seq - EST (expressed sequence tag) sequence entries, part 49.
120. gbest50.seq - EST (expressed sequence tag) sequence entries, part 50.
121. gbest51.seq - EST (expressed sequence tag) sequence entries, part 51.
122. gbest52.seq - EST (expressed sequence tag) sequence entries, part 52.
123. gbest53.seq - EST (expressed sequence tag) sequence entries, part 53.
124. gbest54.seq - EST (expressed sequence tag) sequence entries, part 54.
125. gbest55.seq - EST (expressed sequence tag) sequence entries, part 55.
126. gbest56.seq - EST (expressed sequence tag) sequence entries, part 56.
127. gbest57.seq - EST (expressed sequence tag) sequence entries, part 57.
128. gbest58.seq - EST (expressed sequence tag) sequence entries, part 58.
129. gbest59.seq - EST (expressed sequence tag) sequence entries, part 59.
130. gbest60.seq - EST (expressed sequence tag) sequence entries, part 60.
131. gbest61.seq - EST (expressed sequence tag) sequence entries, part 61.
132. gbest62.seq - EST (expressed sequence tag) sequence entries, part 62.
133. gbest63.seq - EST (expressed sequence tag) sequence entries, part 63.
134. gbest64.seq - EST (expressed sequence tag) sequence entries, part 64.
135. gbest65.seq - EST (expressed sequence tag) sequence entries, part 65.
136. gbest66.seq - EST (expressed sequence tag) sequence entries, part 66.
137. gbest67.seq - EST (expressed sequence tag) sequence entries, part 67.
138. gbest68.seq - EST (expressed sequence tag) sequence entries, part 68.
139. gbest69.seq - EST (expressed sequence tag) sequence entries, part 69.
140. gbest70.seq - EST (expressed sequence tag) sequence entries, part 70.
141. gbest71.seq - EST (expressed sequence tag) sequence entries, part 71.
142. gbest72.seq - EST (expressed sequence tag) sequence entries, part 72.
143. gbest73.seq - EST (expressed sequence tag) sequence entries, part 73.
144. gbest74.seq - EST (expressed sequence tag) sequence entries, part 74.
145. gbest75.seq - EST (expressed sequence tag) sequence entries, part 75.
146. gbest76.seq - EST (expressed sequence tag) sequence entries, part 76.
147. gbest77.seq - EST (expressed sequence tag) sequence entries, part 77.
148. gbest78.seq - EST (expressed sequence tag) sequence entries, part 78.
149. gbest79.seq - EST (expressed sequence tag) sequence entries, part 79.
150. gbest80.seq - EST (expressed sequence tag) sequence entries, part 80.
151. gbest81.seq - EST (expressed sequence tag) sequence entries, part 81.
152. gbest82.seq - EST (expressed sequence tag) sequence entries, part 82.
153. gbest83.seq - EST (expressed sequence tag) sequence entries, part 83.
154. gbest84.seq - EST (expressed sequence tag) sequence entries, part 84.
155. gbest85.seq - EST (expressed sequence tag) sequence entries, part 85.
156. gbest86.seq - EST (expressed sequence tag) sequence entries, part 86.
157. gbest87.seq - EST (expressed sequence tag) sequence entries, part 87.
158. gbest88.seq - EST (expressed sequence tag) sequence entries, part 88.
159. gbest89.seq - EST (expressed sequence tag) sequence entries, part 89
160. gbest90.seq - EST (expressed sequence tag) sequence entries, part 90.
161. gbest91.seq - EST (expressed sequence tag) sequence entries, part 91.
162. gbest92.seq - EST (expressed sequence tag) sequence entries, part 92.
163. gbest93.seq - EST (expressed sequence tag) sequence entries, part 93.
164. gbest94.seq - EST (expressed sequence tag) sequence entries, part 94.
165. gbest95.seq - EST (expressed sequence tag) sequence entries, part 95.
166. gbest96.seq - EST (expressed sequence tag) sequence entries, part 96.
167. gbest97.seq - EST (expressed sequence tag) sequence entries, part 97.
168. gbest98.seq - EST (expressed sequence tag) sequence entries, part 98.
169. gbest99.seq - EST (expressed sequence tag) sequence entries, part 99.
170. gbest100.seq - EST (expressed sequence tag) sequence entries, part 100.
171. gbest101.seq - EST (expressed sequence tag) sequence entries, part 101.
172. gbest102.seq - EST (expressed sequence tag) sequence entries, part 102.
173. gbest103.seq - EST (expressed sequence tag) sequence entries, part 103.
174. gbest104.seq - EST (expressed sequence tag) sequence entries, part 104.
175. gbest105.seq - EST (expressed sequence tag) sequence entries, part 105.
176. gbest106.seq - EST (expressed sequence tag) sequence entries, part 106.
177. gbest107.seq - EST (expressed sequence tag) sequence entries, part 107.
178. gbest108.seq - EST (expressed sequence tag) sequence entries, part 108.
179. gbest109.seq - EST (expressed sequence tag) sequence entries, part 109.
180. gbest110.seq - EST (expressed sequence tag) sequence entries, part 110.
181. gbest111.seq - EST (expressed sequence tag) sequence entries, part 111.
182. gbest112.seq - EST (expressed sequence tag) sequence entries, part 112.
183. gbest113.seq - EST (expressed sequence tag) sequence entries, part 113.
184. gbest114.seq - EST (expressed sequence tag) sequence entries, part 114.
185. gbest115.seq - EST (expressed sequence tag) sequence entries, part 115.
186. gbest116.seq - EST (expressed sequence tag) sequence entries, part 116.
187. gbest117.seq - EST (expressed sequence tag) sequence entries, part 117.
188. gbest118.seq - EST (expressed sequence tag) sequence entries, part 118.
189. gbest119.seq - EST (expressed sequence tag) sequence entries, part 119.
190. gbest120.seq - EST (expressed sequence tag) sequence entries, part 120.
191. gbest121.seq - EST (expressed sequence tag) sequence entries, part 121.
192. gbest122.seq - EST (expressed sequence tag) sequence entries, part 122.
193. gbest123.seq - EST (expressed sequence tag) sequence entries, part 123.
194. gbest124.seq - EST (expressed sequence tag) sequence entries, part 124.
195. gbest125.seq - EST (expressed sequence tag) sequence entries, part 125.
196. gbest126.seq - EST (expressed sequence tag) sequence entries, part 126.
197. gbest127.seq - EST (expressed sequence tag) sequence entries, part 127.
198. gbest128.seq - EST (expressed sequence tag) sequence entries, part 128.
199. gbest129.seq - EST (expressed sequence tag) sequence entries, part 129.
200. gbest130.seq - EST (expressed sequence tag) sequence entries, part 130.
201. gbest131.seq - EST (expressed sequence tag) sequence entries, part 131.
202. gbest132.seq - EST (expressed sequence tag) sequence entries, part 132.
203. gbest133.seq - EST (expressed sequence tag) sequence entries, part 133.
204. gbest134.seq - EST (expressed sequence tag) sequence entries, part 134.
205. gbest135.seq - EST (expressed sequence tag) sequence entries, part 135.
206. gbest136.seq - EST (expressed sequence tag) sequence entries, part 136.
207. gbest137.seq - EST (expressed sequence tag) sequence entries, part 137.
208. gbest138.seq - EST (expressed sequence tag) sequence entries, part 138.
209. gbest139.seq - EST (expressed sequence tag) sequence entries, part 139.
210. gbest140.seq - EST (expressed sequence tag) sequence entries, part 140.
211. gbest141.seq - EST (expressed sequence tag) sequence entries, part 141.
212. gbest142.seq - EST (expressed sequence tag) sequence entries, part 142.
213. gbest143.seq - EST (expressed sequence tag) sequence entries, part 143.
214. gbest144.seq - EST (expressed sequence tag) sequence entries, part 144.
215. gbest145.seq - EST (expressed sequence tag) sequence entries, part 145.
216. gbest146.seq - EST (expressed sequence tag) sequence entries, part 146.
217. gbest147.seq - EST (expressed sequence tag) sequence entries, part 147.
218. gbest148.seq - EST (expressed sequence tag) sequence entries, part 148.
219. gbest149.seq - EST (expressed sequence tag) sequence entries, part 149.
220. gbest150.seq - EST (expressed sequence tag) sequence entries, part 150.
221. gbest151.seq - EST (expressed sequence tag) sequence entries, part 151.
222. gbest152.seq - EST (expressed sequence tag) sequence entries, part 152.
223. gbest153.seq - EST (expressed sequence tag) sequence entries, part 153.
224. gbest154.seq - EST (expressed sequence tag) sequence entries, part 154.
225. gbest155.seq - EST (expressed sequence tag) sequence entries, part 155.
226. gbest156.seq - EST (expressed sequence tag) sequence entries, part 156.
227. gbest157.seq - EST (expressed sequence tag) sequence entries, part 157.
228. gbest158.seq - EST (expressed sequence tag) sequence entries, part 158.
229. gbest159.seq - EST (expressed sequence tag) sequence entries, part 159.
230. gbest160.seq - EST (expressed sequence tag) sequence entries, part 160.
231. gbest161.seq - EST (expressed sequence tag) sequence entries, part 161.
232. gbest162.seq - EST (expressed sequence tag) sequence entries, part 162.
233. gbest163.seq - EST (expressed sequence tag) sequence entries, part 163.
234. gbest164.seq - EST (expressed sequence tag) sequence entries, part 164.
235. gbest165.seq - EST (expressed sequence tag) sequence entries, part 165.
236. gbest166.seq - EST (expressed sequence tag) sequence entries, part 166.
237. gbest167.seq - EST (expressed sequence tag) sequence entries, part 167.
238. gbest168.seq - EST (expressed sequence tag) sequence entries, part 168.
239. gbest169.seq - EST (expressed sequence tag) sequence entries, part 169.
240. gbest170.seq - EST (expressed sequence tag) sequence entries, part 170.
241. gbest171.seq - EST (expressed sequence tag) sequence entries, part 171.
242. gbest172.seq - EST (expressed sequence tag) sequence entries, part 172.
243. gbest173.seq - EST (expressed sequence tag) sequence entries, part 173.
244. gbest174.seq - EST (expressed sequence tag) sequence entries, part 174.
245. gbest175.seq - EST (expressed sequence tag) sequence entries, part 175.
246. gbest176.seq - EST (expressed sequence tag) sequence entries, part 176.
247. gbest177.seq - EST (expressed sequence tag) sequence entries, part 177.
248. gbest178.seq - EST (expressed sequence tag) sequence entries, part 178.
249. gbpat1.seq  - Patent sequence entries, part 1.
250. gbpat2.seq  - Patent sequence entries, part 2.
251. gbpat3.seq  - Patent sequence entries, part 3.
252. gbpat4.seq  - Patent sequence entries, part 4.
253. gbpat5.seq  - Patent sequence entries, part 5.
254. gbsts1.seq  - STS (sequence tagged site) sequence entries, part 1.
255. gbsts2.seq  - STS (sequence tagged site) sequence entries, part 2.
256. gbgss1.seq  - GSS (genome survey sequence) sequence entries, part 1.
257. gbgss2.seq  - GSS (genome survey sequence) sequence entries, part 2.
258. gbgss3.seq  - GSS (genome survey sequence) sequence entries, part 3.
259. gbgss4.seq  - GSS (genome survey sequence) sequence entries, part 4.
260. gbgss5.seq  - GSS (genome survey sequence) sequence entries, part 5.
261. gbgss6.seq  - GSS (genome survey sequence) sequence entries, part 6.
262. gbgss7.seq  - GSS (genome survey sequence) sequence entries, part 7.
263. gbgss8.seq  - GSS (genome survey sequence) sequence entries, part 8.
264. gbgss9.seq  - GSS (genome survey sequence) sequence entries, part 9.
265. gbgss10.seq - GSS (genome survey sequence) sequence entries, part 10.
266. gbgss11.seq - GSS (genome survey sequence) sequence entries, part 11.
267. gbgss12.seq - GSS (genome survey sequence) sequence entries, part 12.
268. gbgss13.seq - GSS (genome survey sequence) sequence entries, part 13.
269. gbgss14.seq - GSS (genome survey sequence) sequence entries, part 14.
270. gbgss15.seq - GSS (genome survey sequence) sequence entries, part 15.
271. gbgss16.seq - GSS (genome survey sequence) sequence entries, part 16.
272. gbgss17.seq - GSS (genome survey sequence) sequence entries, part 17.
273. gbgss18.seq - GSS (genome survey sequence) sequence entries, part 18.
274. gbgss19.seq - GSS (genome survey sequence) sequence entries, part 19.
275. gbgss20.seq - GSS (genome survey sequence) sequence entries, part 20.
276. gbgss21.seq - GSS (genome survey sequence) sequence entries, part 21.
277. gbgss22.seq - GSS (genome survey sequence) sequence entries, part 22.
278. gbgss23.seq - GSS (genome survey sequence) sequence entries, part 23.
279. gbgss24.seq - GSS (genome survey sequence) sequence entries, part 24.
280. gbgss25.seq - GSS (genome survey sequence) sequence entries, part 25.
281. gbgss26.seq - GSS (genome survey sequence) sequence entries, part 26.
282. gbgss27.seq - GSS (genome survey sequence) sequence entries, part 27.
283. gbgss28.seq - GSS (genome survey sequence) sequence entries, part 28.
284. gbgss29.seq - GSS (genome survey sequence) sequence entries, part 29.
285. gbgss30.seq - GSS (genome survey sequence) sequence entries, part 30.
286. gbgss31.seq - GSS (genome survey sequence) sequence entries, part 31.
287. gbgss32.seq - GSS (genome survey sequence) sequence entries, part 32.
288. gbgss33.seq - GSS (genome survey sequence) sequence entries, part 33.
289. gbgss34.seq - GSS (genome survey sequence) sequence entries, part 34.
290. gbgss35.seq - GSS (genome survey sequence) sequence entries, part 35.
291. gbgss36.seq - GSS (genome survey sequence) sequence entries, part 36.
292. gbgss37.seq - GSS (genome survey sequence) sequence entries, part 37.
293. gbgss38.seq - GSS (genome survey sequence) sequence entries, part 38.
294. gbgss39.seq - GSS (genome survey sequence) sequence entries, part 39.
295. gbgss40.seq - GSS (genome survey sequence) sequence entries, part 40.
296. gbgss41.seq - GSS (genome survey sequence) sequence entries, part 41.
297. gbgss42.seq - GSS (genome survey sequence) sequence entries, part 42.
298. gbgss43.seq - GSS (genome survey sequence) sequence entries, part 43.
299. gbgss44.seq - GSS (genome survey sequence) sequence entries, part 44.
300. gbgss45.seq - GSS (genome survey sequence) sequence entries, part 45.
301. gbgss46.seq - GSS (genome survey sequence) sequence entries, part 46.
302. gbgss47.seq - GSS (genome survey sequence) sequence entries, part 47.
303. gbgss48.seq - GSS (genome survey sequence) sequence entries, part 48.
304. gbgss49.seq - GSS (genome survey sequence) sequence entries, part 49.
305. gbgss50.seq - GSS (genome survey sequence) sequence entries, part 50.
306. gbgss51.seq - GSS (genome survey sequence) sequence entries, part 51.
307. gbgss52.seq - GSS (genome survey sequence) sequence entries, part 52.
308. gbhtg1.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 1.
309. gbhtg2.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 2.
310. gbhtg3.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 3.
311. gbhtg4.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 4.
312. gbhtg5.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 5.
313. gbhtg6.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 6.
314. gbhtg7.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 7.
315. gbhtg8.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 8.
316. gbhtg9.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 9.
317. gbhtg10.seq - HTGS (high throughput genomic sequencing) sequence entries, part 10.
318. gbhtg11.seq - HTGS (high throughput genomic sequencing) sequence entries, part 11.
319. gbhtg12.seq - HTGS (high throughput genomic sequencing) sequence entries, part 12.
320. gbhtg13.seq - HTGS (high throughput genomic sequencing) sequence entries, part 13.
321. gbhtg14.seq - HTGS (high throughput genomic sequencing) sequence entries, part 14.
322. gbhtg15.seq - HTGS (high throughput genomic sequencing) sequence entries, part 15.
323. gbhtg16.seq - HTGS (high throughput genomic sequencing) sequence entries, part 16.
324. gbhtg17.seq - HTGS (high throughput genomic sequencing) sequence entries, part 17.
325. gbhtg18.seq - HTGS (high throughput genomic sequencing) sequence entries, part 18.
326. gbhtg19.seq - HTGS (high throughput genomic sequencing) sequence entries, part 19.
327. gbhtg20.seq - HTGS (high throughput genomic sequencing) sequence entries, part 20.
328. gbhtg21.seq - HTGS (high throughput genomic sequencing) sequence entries, part 21.
329. gbhtg22.seq - HTGS (high throughput genomic sequencing) sequence entries, part 22.
330. gbhtg23.seq - HTGS (high throughput genomic sequencing) sequence entries, part 23.
331. gbhtg24.seq - HTGS (high throughput genomic sequencing) sequence entries, part 24.
332. gbhtg25.seq - HTGS (high throughput genomic sequencing) sequence entries, part 25.
333. gbhtg26.seq - HTGS (high throughput genomic sequencing) sequence entries, part 26.
334. gbhtg27.seq - HTGS (high throughput genomic sequencing) sequence entries, part 27.
335. gbhtg28.seq - HTGS (high throughput genomic sequencing) sequence entries, part 28.
336. gbhtg29.seq - HTGS (high throughput genomic sequencing) sequence entries, part 29.
337. gbhtg30.seq - HTGS (high throughput genomic sequencing) sequence entries, part 30.
338. gbhtg31.seq - HTGS (high throughput genomic sequencing) sequence entries, part 31.
339. gbhtg32.seq - HTGS (high throughput genomic sequencing) sequence entries, part 32.
340. gbhtg33.seq - HTGS (high throughput genomic sequencing) sequence entries, part 33.
341. gbhtg34.seq - HTGS (high throughput genomic sequencing) sequence entries, part 34.
342. gbhtg35.seq - HTGS (high throughput genomic sequencing) sequence entries, part 35.
343. gbhtg36.seq - HTGS (high throughput genomic sequencing) sequence entries, part 36.
344. gbhtg37.seq - HTGS (high throughput genomic sequencing) sequence entries, part 37.
345. gbhtg38.seq - HTGS (high throughput genomic sequencing) sequence entries, part 38.
346. gbhtg39.seq - HTGS (high throughput genomic sequencing) sequence entries, part 39.
347. gbhtg40.seq - HTGS (high throughput genomic sequencing) sequence entries, part 40.
348. gbhtg41.seq - HTGS (high throughput genomic sequencing) sequence entries, part 41.
349. gbhtg42.seq - HTGS (high throughput genomic sequencing) sequence entries, part 42.
350. gbhtg43.seq - HTGS (high throughput genomic sequencing) sequence entries, part 43.
351. gbhtc.seq	 - HTC (high throughput cDNA sequencing) entries.

  Three Supplemental files provide the accession numbers of GenBank entries
that are new, updated, or deleted since the previous release:

a.  gbchg.txt	- Entries updated since the previous release.
b.  gbdel.txt	- Entries deleted since the previous release.
c.  gbnew.txt	- Entries new since the previous release.

  An experimental file called gbcon.seq provides an alternative representation
for complex sequences, such as "segmented sets" and complete-genomes that have
been split into pieces. The GenBank README describes the experimental CON
division of GenBank in more detail:

	ftp://ftp.ncbi.nih.gov/genbank/README.genbank

2.2.5 File Sizes

  Uncompressed, the Release 131.0 flatfiles require roughly 74.82 GB (sequence
files only) or 83.65 GB (including the 'short directory' and 'index' files).
The following table contains the approximate sizes of the individual files in
this release.  Since minor changes to some of the files might have occurred
after these release notes were written, these sizes should not be used to
determine file integrity; they are provided as an aid to planning only.

File Size      File Name

 593173207     gbacc.idx
 507258883     gbaut1.idx
 503164605     gbaut10.idx
 500087767     gbaut11.idx
 337716862     gbaut12.idx
 500315561     gbaut2.idx
 500013566     gbaut3.idx
 509265498     gbaut4.idx
 503657117     gbaut5.idx
 519750591     gbaut6.idx
 504967435     gbaut7.idx
 501038148     gbaut8.idx
 501005175     gbaut9.idx
 250009587     gbbct1.seq
 250002888     gbbct2.seq
 250436888     gbbct3.seq
 250059753     gbbct4.seq
 195865415     gbbct5.seq
   3283314     gbchg.txt
  14492673     gbcon.seq
     78845     gbdel.txt
 230687626     gbest1.seq
 230689595     gbest10.seq
 230687468     gbest100.seq
 230690761     gbest101.seq
 230687496     gbest102.seq
 230687975     gbest103.seq
 230689813     gbest104.seq
 230690091     gbest105.seq
 229132554     gbest106.seq
 230689282     gbest107.seq
 230691004     gbest108.seq
 230690093     gbest109.seq
 230689197     gbest11.seq
 230688320     gbest110.seq
 230687835     gbest111.seq
 230687833     gbest112.seq
 230689138     gbest113.seq
 230689322     gbest114.seq
 230688491     gbest115.seq
 230688940     gbest116.seq
 230689815     gbest117.seq
 230689628     gbest118.seq
 230689149     gbest119.seq
 230690329     gbest12.seq
 230687652     gbest120.seq
 227367674     gbest121.seq
 230689976     gbest122.seq
 230689424     gbest123.seq
 230688145     gbest124.seq
 230689678     gbest125.seq
 230690424     gbest126.seq
 230687780     gbest127.seq
 230688567     gbest128.seq
 230689037     gbest129.seq
 230688573     gbest13.seq
 230689488     gbest130.seq
 230688531     gbest131.seq
 230691065     gbest132.seq
 230690252     gbest133.seq
 230687524     gbest134.seq
 230689384     gbest135.seq
 230688321     gbest136.seq
 230687967     gbest137.seq
 230688894     gbest138.seq
 230687914     gbest139.seq
 230689163     gbest14.seq
 230689218     gbest140.seq
 230687968     gbest141.seq
 230690072     gbest142.seq
 230690504     gbest143.seq
 230689666     gbest144.seq
 230691513     gbest145.seq
 230688687     gbest146.seq
 230689542     gbest147.seq
 230689957     gbest148.seq
 230689853     gbest149.seq
 230689736     gbest15.seq
 230688217     gbest150.seq
 230688810     gbest151.seq
 230689266     gbest152.seq
 230688541     gbest153.seq
 230687727     gbest154.seq
 230688742     gbest155.seq
 230688315     gbest156.seq
 230689537     gbest157.seq
 230688312     gbest158.seq
 230688338     gbest159.seq
 230687917     gbest16.seq
 230387189     gbest160.seq
 230688857     gbest161.seq
 230688654     gbest162.seq
 230689442     gbest163.seq
 230688044     gbest164.seq
 230690016     gbest165.seq
 230688996     gbest166.seq
 230691099     gbest167.seq
 230688354     gbest168.seq
 230688732     gbest169.seq
 230688427     gbest17.seq
 230689548     gbest170.seq
 230688125     gbest171.seq
 230687506     gbest172.seq
 230690389     gbest173.seq
 230688874     gbest174.seq
 223292119     gbest175.seq
 230687945     gbest176.seq
 230687913     gbest177.seq
   9251483     gbest178.seq
 230688469     gbest18.seq
 230688175     gbest19.seq
 230124030     gbest2.seq
 230688363     gbest20.seq
 230688714     gbest21.seq
 230689980     gbest22.seq
 230689378     gbest23.seq
 230690697     gbest24.seq
 230688418     gbest25.seq
 230688312     gbest26.seq
 230689485     gbest27.seq
 230687536     gbest28.seq
 230687847     gbest29.seq
 230688851     gbest3.seq
 230688767     gbest30.seq
 230687479     gbest31.seq
 230688502     gbest32.seq
 230688719     gbest33.seq
 230688010     gbest34.seq
 209749805     gbest35.seq
 208893992     gbest36.seq
 215313294     gbest37.seq
 215000275     gbest38.seq
 215957191     gbest39.seq
 230688715     gbest4.seq
 216291385     gbest40.seq
 218968248     gbest41.seq
 230687541     gbest42.seq
 230688389     gbest43.seq
 214258574     gbest44.seq
 230689640     gbest45.seq
 230687690     gbest46.seq
 230688113     gbest47.seq
 230691084     gbest48.seq
 230690518     gbest49.seq
 163938665     gbest5.seq
 230688400     gbest50.seq
 230688566     gbest51.seq
 230688553     gbest52.seq
 230690055     gbest53.seq
 230688705     gbest54.seq
 230689630     gbest55.seq
 230688231     gbest56.seq
 230689637     gbest57.seq
 230689015     gbest58.seq
 230689347     gbest59.seq
 181346921     gbest6.seq
 216775886     gbest60.seq
 208976108     gbest61.seq
 208582263     gbest62.seq
 208563326     gbest63.seq
 208964607     gbest64.seq
 210367818     gbest65.seq
 208808344     gbest66.seq
 208365749     gbest67.seq
 209650681     gbest68.seq
 209502143     gbest69.seq
 230689256     gbest7.seq
 204780744     gbest70.seq
 207240696     gbest71.seq
 206679469     gbest72.seq
 209054063     gbest73.seq
 220007084     gbest74.seq
 230692016     gbest75.seq
 230689546     gbest76.seq
 230690564     gbest77.seq
 223592183     gbest78.seq
 226075109     gbest79.seq
 230689501     gbest8.seq
 226278296     gbest80.seq
 230688905     gbest81.seq
 230689687     gbest82.seq
 230687776     gbest83.seq
 230689325     gbest84.seq
 230688460     gbest85.seq
 230687883     gbest86.seq
 230688295     gbest87.seq
 230689562     gbest88.seq
 230687837     gbest89.seq
 230690317     gbest9.seq
 230690126     gbest90.seq
 230690257     gbest91.seq
 230688344     gbest92.seq
 230689887     gbest93.seq
 230688247     gbest94.seq
 230689837     gbest95.seq
 230689990     gbest96.seq
 230687463     gbest97.seq
 230688940     gbest98.seq
 230687848     gbest99.seq
  24863049     gbgen.idx
 209717880     gbgss1.seq
 209716032     gbgss10.seq
 209718664     gbgss11.seq
 209715966     gbgss12.seq
 209717342     gbgss13.seq
 209718066     gbgss14.seq
 209717771     gbgss15.seq
 209715956     gbgss16.seq
 209717978     gbgss17.seq
 209718536     gbgss18.seq
 209719543     gbgss19.seq
 209718693     gbgss2.seq
 209716591     gbgss20.seq
 209719818     gbgss21.seq
 209719439     gbgss22.seq
 209718210     gbgss23.seq
 209717151     gbgss24.seq
 209719135     gbgss25.seq
 209716240     gbgss26.seq
 209718778     gbgss27.seq
 209716045     gbgss28.seq
 209716173     gbgss29.seq
 209717154     gbgss3.seq
 209719080     gbgss30.seq
 209716489     gbgss31.seq
 209718568     gbgss32.seq
 209716016     gbgss33.seq
 209717983     gbgss34.seq
 209717445     gbgss35.seq
 209718471     gbgss36.seq
 209718413     gbgss37.seq
 209716483     gbgss38.seq
 209717945     gbgss39.seq
 209716319     gbgss4.seq
 209716946     gbgss40.seq
 209716774     gbgss41.seq
 209718199     gbgss42.seq
 209717537     gbgss43.seq
 119931626     gbgss44.seq
 250002532     gbgss45.seq
 250000812     gbgss46.seq
 250000747     gbgss47.seq
 250000726     gbgss48.seq
 250000351     gbgss49.seq
 209716604     gbgss5.seq
 250004323     gbgss50.seq
 250000449     gbgss51.seq
 247404521     gbgss52.seq
 209718331     gbgss6.seq
 209716656     gbgss7.seq
 209718361     gbgss8.seq
 209718181     gbgss9.seq
 238289359     gbhtc.seq
 250210107     gbhtg1.seq
 250100421     gbhtg10.seq
 250029514     gbhtg11.seq
 250152594     gbhtg12.seq
 250267792     gbhtg13.seq
 250173231     gbhtg14.seq
 250024483     gbhtg15.seq
 250119863     gbhtg16.seq
 250016390     gbhtg17.seq
 250215610     gbhtg18.seq
 250108040     gbhtg19.seq
 250010219     gbhtg2.seq
 250123134     gbhtg20.seq
 250019373     gbhtg21.seq
 250149136     gbhtg22.seq
 250255518     gbhtg23.seq
 250186813     gbhtg24.seq
 250214060     gbhtg25.seq
 250177955     gbhtg26.seq
 250319461     gbhtg27.seq
 250023542     gbhtg28.seq
 250026849     gbhtg29.seq
 250103501     gbhtg3.seq
 250140518     gbhtg30.seq
 250017223     gbhtg31.seq
 250210169     gbhtg32.seq
 250244260     gbhtg33.seq
 250314399     gbhtg34.seq
 250225401     gbhtg35.seq
 250145993     gbhtg36.seq
 250036798     gbhtg37.seq
 250125092     gbhtg38.seq
 250179347     gbhtg39.seq
 250041184     gbhtg4.seq
 250146495     gbhtg40.seq
 250057339     gbhtg41.seq
 250068604     gbhtg42.seq
 223215113     gbhtg43.seq
 250068814     gbhtg5.seq
 250001698     gbhtg6.seq
 250123658     gbhtg7.seq
 250120520     gbhtg8.seq
 250058792     gbhtg9.seq
 250043702     gbinv1.seq
 250066852     gbinv2.seq
 250007253     gbinv3.seq
 250004152     gbinv4.seq
 113988943     gbinv5.seq
 440034397     gbjou.idx
 406665298     gbkey.idx
 138153484     gbmam.seq
  11360918     gbnew.txt
 250000039     gbpat1.seq
 250000449     gbpat2.seq
 250114519     gbpat3.seq
 250000584     gbpat4.seq
  85752401     gbpat5.seq
  18514286     gbphg.seq
 250001106     gbpln1.seq
 250000915     gbpln2.seq
 250327811     gbpln3.seq
 250002487     gbpln4.seq
 250000354     gbpln5.seq
 120252537     gbpln6.seq
 250079499     gbpri1.seq
 250118699     gbpri10.seq
 250074958     gbpri11.seq
 250106445     gbpri12.seq
 250138913     gbpri13.seq
 250076053     gbpri14.seq
 250114774     gbpri15.seq
 250056927     gbpri16.seq
 250121612     gbpri17.seq
 250113782     gbpri18.seq
 250022632     gbpri19.seq
 250024358     gbpri2.seq
 250049898     gbpri20.seq
 250001341     gbpri21.seq
 162464452     gbpri22.seq
 250014147     gbpri3.seq
 250156648     gbpri4.seq
 250084430     gbpri5.seq
 250136114     gbpri6.seq
 250231184     gbpri7.seq
 250172396     gbpri8.seq
 250005543     gbpri9.seq
    128430     gbrel.txt
 250001935     gbrod1.seq
 250017224     gbrod2.seq
 250003853     gbrod3.seq
 164287156     gbrod4.seq
1455791363     gbsdr.txt
   1359853     gbsec.idx
 250000709     gbsts1.seq
  90163375     gbsts2.seq
  32170579     gbsyn.seq
   1194911     gbuna.seq
 250002188     gbvrl1.seq
 250229890     gbvrl2.seq
  44849544     gbvrl3.seq
 250003236     gbvrt1.seq
  34256307     gbvrt2.seq

2.2.6 Per-Division Statistics 

  The following table provides a per-division breakdown of the number of
sequence entries and the total number of bases of DNA/RNA in each sequence
data file:

Division     Entries    Bases

BCT1         19841      103009067
BCT2         30789      97960698
BCT3         36010      98433013
BCT4         37830      98544076
BCT5         30456      71100105
EST1         68775      26546702
EST10        76865      29915887
EST100       70814      33035820
EST101       65030      33861674
EST102       69302      40922065
EST103       71863      46887423
EST104       76480      33477728
EST105       74971      30836920
EST106       76200      25951521
EST107       74293      35664675
EST108       66161      37721608
EST109       79990      44832889
EST11        76732      29136099
EST110       79955      45471493
EST111       73779      46386260
EST112       69323      43475258
EST113       73553      48243473
EST114       68547      45153017
EST115       74708      44713334
EST116       74192      44542246
EST117       74467      48258750
EST118       73791      48349760
EST119       73880      46229251
EST12        77209      30848014
EST120       79002      40452495
EST121       76132      25203765
EST122       83065      48285876
EST123       75909      44779365
EST124       68535      38827027
EST125       70238      34773025
EST126       70270      38730373
EST127       66688      36388404
EST128       71861      44382308
EST129       73322      45393531
EST13        78569      30349956
EST130       68470      39819722
EST131       69300      40378014
EST132       75842      46013946
EST133       68221      39999246
EST134       63109      36004665
EST135       92233      50085318
EST136       80344      46267417
EST137       72663      37288577
EST138       101274     53748626
EST139       102089     56264757
EST14        78853      31591328
EST140       80417      47542872
EST141       65594      34384677
EST142       64247      29505961
EST143       55773      28736664
EST144       66139      32583258
EST145       60515      30647299
EST146       69891      38372538
EST147       70504      49367415
EST148       68490      47905311
EST149       79420      46068883
EST15        73227      31048665
EST150       58578      30229294
EST151       64651      32984559
EST152       67445      39237129
EST153       66792      45734513
EST154       62801      36017528
EST155       75141      40100233
EST156       66710      45086741
EST157       68682      39115916
EST158       62144      41960902
EST159       69137      32799821
EST16        75585      33149814
EST160       75593      28021731
EST161       72181      46004209
EST162       72524      37450025
EST163       63447      33898983
EST164       71627      54116749
EST165       67868      42234768
EST166       70003      35328889
EST167       69900      53682031
EST168       68766      46333333
EST169       92707      34852241
EST17        85033      34425673
EST170       105984     37825693
EST171       75276      26189931
EST172       72956      26878358
EST173       74284      26449042
EST174       73422      26754825
EST175       78161      26253031
EST176       72711      28960454
EST177       73862      28313304
EST178       3879       1337400
EST18        79506      32466481
EST19        81674      34032432
EST2         75443      28959086
EST20        72793      29417006
EST21        72878      33707030
EST22        77415      30819584
EST23        76811      31867281
EST24        75688      34539312
EST25        73354      31008435
EST26        76095      31264094
EST27        79985      35697587
EST28        99385      46732989
EST29        72729      52421527
EST3         74283      30177020
EST30        85273      55356701
EST31        94468      49566058
EST32        95814      42532090
EST33        95577      49290817
EST34        87632      35378192
EST35        59417      15947228
EST36        59636      15942110
EST37        70027      20758656
EST38        43605      12050158
EST39        43414      11891156
EST4         74704      28164602
EST40        43047      12076099
EST41        46932      13916252
EST42        101654     44489665
EST43        95633      45302318
EST44        86121      46185141
EST45        91198      42990892
EST46        105353     55233224
EST47        80414      37308227
EST48        71776      30329222
EST49        70908      31359017
EST5         48621      15382308
EST50        74588      32346390
EST51        74321      31243534
EST52        83305      32056446
EST53        69291      27851386
EST54        64237      29983561
EST55        72922      31897216
EST56        81499      36999224
EST57        74772      30414929
EST58        75004      26605951
EST59        88463      40938896
EST6         56778      18491938
EST60        49134      16215916
EST61        40178      11121075
EST62        40207      11991608
EST63        40510      12505653
EST64        40606      12194537
EST65        40517      13021587
EST66        40580      12679743
EST67        40441      12315959
EST68        40152      12096497
EST69        40616      12676247
EST7         74818      29465337
EST70        41480      11809084
EST71        41254      13098695
EST72        41117      12674611
EST73        41008      13509506
EST74        45730      11902343
EST75        40429      24921319
EST76        42003      22046434
EST77        42482      17478878
EST78        46083      21157403
EST79        45231      18695822
EST8         76985      30934326
EST80        44914      19369839
EST81        74796      32484933
EST82        74456      29119148
EST83        73398      30575144
EST84        77955      44848578
EST85        78781      41818118
EST86        76792      40780847
EST87        79420      38589588
EST88        70384      41033976
EST89        74955      35392503
EST9         77992      30133271
EST90        75528      38241920
EST91        70901      37160777
EST92        78154      51085571
EST93        67601      34963478
EST94        72950      36812231
EST95        72717      40059245
EST96        74656      44776493
EST97        70441      44420784
EST98        74431      42559444
EST99        69727      29467762
GSS1         83824      35929461
GSS10        67053      35981043
GSS11        70614      39736728
GSS12        61939      32332805
GSS13        68007      35364486
GSS14        68307      34833716
GSS15        66054      29679106
GSS16        64193      31894967
GSS17        72798      43609075
GSS18        65728      30769184
GSS19        57864      26820930
GSS2         83834      36234779
GSS20        52347      27229503
GSS21        53008      25511573
GSS22        53984      22994846
GSS23        59459      37840294
GSS24        57313      26713897
GSS25        53405      25269553
GSS26        64387      41456419
GSS27        61017      24507694
GSS28        53785      23468937
GSS29        59982      29437031
GSS3         83132      38797491
GSS30        62279      30367764
GSS31        64231      35921785
GSS32        81978      36215066
GSS33        69587      37317292
GSS34        66514      41675071
GSS35        67225      38431339
GSS36        74277      37277325
GSS37        70348      37503520
GSS38        76134      42802670
GSS39        86250      57275671
GSS4         75089      38552272
GSS40        85816      55789071
GSS41        81060      43085285
GSS42        79946      45066529
GSS43        81453      33658562
GSS44        42604      16876222
GSS45        85554      65201473
GSS46        82043      61580241
GSS47        79976      51094898
GSS48        79900      67021368
GSS49        75458      63565275
GSS5         72268      38643781
GSS50        70639      66724063
GSS51        72654      54285052
GSS52        106018     49109969
GSS6         70416      35264228
GSS7         72384      36330712
GSS8         71884      36782770
GSS9         68978      34210350
HTC          37838      46652705
HTG1         1318       191061702
HTG10        1129       190514686
HTG11        1278       189098183
HTG12        1469       187280987
HTG13        1213       189182898
HTG14        1202       185246171
HTG15        1273       185442522
HTG16        1283       185329066
HTG17        1784       181595344
HTG18        1580       183067525
HTG19        1421       184803361
HTG2         1737       188547919
HTG20        1459       185328304
HTG21        1266       185687170
HTG22        1335       186253447
HTG23        1266       186432773
HTG24        1326       184858019
HTG25        1213       186957996
HTG26        1255       186600924
HTG27        1339       186513173
HTG28        1335       185542945
HTG29        1473       184158715
HTG3         2676       187400744
HTG30        1444       184451038
HTG31        1127       190439689
HTG32        1284       187416171
HTG33        1154       190351697
HTG34        1216       187488338
HTG35        1161       188589970
HTG36        1230       186323041
HTG37        1391       185887963
HTG38        1538       186897591
HTG39        1146       192818146
HTG4         3137       190272802
HTG40        968        194331137
HTG41        1072       192101553
HTG42        1306       192325296
HTG43        1181       170302871
HTG5         1288       188788769
HTG6         1280       187897480
HTG7         1234       188762462
HTG8         1240       188149587
HTG9         1289       187935443
INV1         8131       176575228
INV2         3972       166158366
INV3         71742      81904792
INV4         32117      113168112
INV5         18539      48692380
MAM          41615      46599250
PAT1         224349     70522689
PAT2         153269     86170906
PAT3         117022     111999260
PAT4         130983     83205920
PAT5         78267      21936926
PHG          2173       7046721
PLN1         18825      141861922
PLN2         77643      78744767
PLN3         27259      137580525
PLN4         45842      83637513
PLN5         51051      106423711
PLN6         19573      50384495
PRI1         13084      156131802
PRI10        1301       174503163
PRI11        1551       176103714
PRI12        25074      144364322
PRI13        37897      118958219
PRI14        1615       177893862
PRI15        1649       180882317
PRI16        1917       182468585
PRI17        1972       187248032
PRI18        23614      141509303
PRI19        13828      164913039
PRI2         1419       173735251
PRI20        44626      121622474
PRI21        32139      130502272
PRI22        39755      63204866
PRI3         1272       183815105
PRI4         1237       175963083
PRI5         1154       175684302
PRI6         1230       181229299
PRI7         1227       170590601
PRI8         1241       172502409
PRI9         1406       176449050
ROD1         13821      168212019
ROD2         14243      171967027
ROD3         15863      161892668
ROD4         43779      57111056
STS1         87862      34710847
STS2         36202      14366421
SYN          7108       13199204
UNA          612        259561
VRL1         74402      63133211
VRL2         76033      64934914
VRL3         10794      15149608
VRT1         69999      85719746
VRT2         10855      10237954

2.2.7 Selected Per-Organism Statistics 

  The following table provides the number of entries and bases of DNA/RNA for
the twenty most sequenced organisms in Release 131.0 (chloroplast and mitochon-
drial sequences not included):

Entries      Bases   Species

5910385 8975089696   Homo sapiens
3693368 4248000223   Mus musculus
440177  2845643085   Rattus norvegicus
334184   684138071   Drosophila melanogaster
364947   340669960   Arabidopsis thaliana
73786    324515226   Oryza sativa (japonica cultivar-group)
196469   220265073   Caenorhabditis elegans
280958   200452421   Danio rerio
140766   196468644   Oryza sativa
299860   195352078   Brassica oleracea
189102   169109095   Tetraodon nigroviridis
160484   161781732   Pan troglodytes
319238   148070112   Zea mays
279229   128872165   Glycine max
242987   128784744   Bos taurus
219188   115991395   Xenopus laevis
174573   112789672   Medicago truncatula
205617   103041525   Triticum aestivum
179025    99099713   Hordeum vulgare
155282    95915175   Anopheles gambiae

2.2.8 Growth of GenBank

  The following table lists the number of bases and the number of sequence
records in each release of GenBank, beginning with Release 3 in 1982.
From 1982 to the present, the number of bases in GenBank has doubled
approximately every 14 months.

Release      Date     Base Pairs   Entries

    3    Dec 1982         680338       606
   14    Nov 1983        2274029      2427
   20    May 1984        3002088      3665
   24    Sep 1984        3323270      4135
   25    Oct 1984        3368765      4175
   26    Nov 1984        3689752      4393
   32    May 1985        4211931      4954
   36    Sep 1985        5204420      5700
   40    Feb 1986        5925429      6642
   42    May 1986        6765476      7416
   44    Aug 1986        8442357      8823
   46    Nov 1986        9615371      9978
   48    Feb 1987       10961380     10913
   50    May 1987       13048473     12534
   52    Aug 1987       14855145     14020
   53    Sep 1987       15514776     14584
   54    Dec 1987       16752872     15465
   55    Mar 1988       19156002     17047
   56    Jun 1988       20795279     18226
   57    Sep 1988       22019698     19044
   57.1  Oct 1988       23800000     20579
   58    Dec 1988       24690876     21248
   59    Mar 1989       26382491     22479
   60    Jun 1989       31808784     26317
   61    Sep 1989       34762585     28791
   62    Dec 1989       37183950     31229
   63    Mar 1990       40127752     33377
   64    Jun 1990       42495893     35100
   65    Sep 1990       49179285     39533
   66    Dec 1990       51306092     41057
   67    Mar 1991       55169276     43903
   68    Jun 1991       65868799     51418
   69    Sep 1991       71947426     55627
   70    Dec 1991       77337678     58952
   71    Mar 1992       83894652     65100
   72    Jun 1992       92160761     71280
   73    Sep 1992      101008486     78608
   74    Dec 1992      120242234     97084
   75    Feb 1993      126212259    106684
   76    Apr 1993      129968355    111911
   77    Jun 1993      138904393    120134
   78    Aug 1993      147215633    131328
   79    Oct 1993      157152442    143492
   80    Dec 1993      163802597    150744
   81    Feb 1994      173261500    162946
   82    Apr 1994      180589455    169896
   83    Jun 1994      191393939    182753
   84    Aug 1994      201815802    196703
   85    Oct 1994      217102462    215273
   86    Dec 1994      230485928    237775
   87    Feb 1995      248499214    269478
   88    Apr 1995      286094556    352414
   89    Jun 1995      318624568    425211
   90    Aug 1995      353713490    492483
   91    Oct 1995      384939485    555694
   92    Dec 1995      425860958    620765
   93    Feb 1996      463758833    685693
   94    Apr 1996      499127741    744295
   95    Jun 1996      551750920    835487
   96    Aug 1996      602072354    920588
   97    Oct 1996      651972984    1021211
   98    Dec 1996      730552938    1114581
   99    Feb 1997      786898138    1192505
   100   Apr 1997      842864309    1274747
   101   Jun 1997      966993087    1491069
   102   Aug 1997     1053474516    1610848
   103   Oct 1997     1160300687    1765847
   104   Dec 1997     1258290513    1891953
   105   Feb 1998     1372368913    2042325
   106   Apr 1998     1502542306    2209232
   107   Jun 1998     1622041465    2355928
   108   Aug 1998     1797137713    2532359
   109   Oct 1998     2008761784    2837897
   110   Dec 1998     2162067871    3043729
   111   Apr 1999     2569578208    3525418
   112   Jun 1999     2974791993    4028171
   113   Aug 1999     3400237391    4610118
   114   Oct 1999     3841163011    4864570
   115   Dec 1999     4653932745    5354511
   116   Feb 2000     5805414935    5691170
   117   Apr 2000     7376080723    6215002
   118   Jun 2000     8604221980    7077491
   119   Aug 2000     9545724824    8214339
   120   Oct 2000    10335692655    9102634
   121   Dec 2000    11101066288    10106023
   122   Feb 2001    11720120326    10896781
   123   Apr 2001    12418544023    11545572
   124   Jun 2001    12973707065    12243766
   125   Aug 2001    13543364296    12813516
   126   Oct 2001    14396883064    13602262
   127   Dec 2001    15849921438    14976310
   128   Feb 2002    17089143893    15465325
   129   Apr 2002    19072679701    16769983
   130   Jun 2002    20648748345    17471130
   131   Aug 2002    22616937182    18197119

3. FILE FORMATS

  The flat file examples included in this section, while not always from the
current release, are usually fairly recent.  Any differences compared to the
actual records are the result of updates to the entries involved.

3.1 File Header Information

  With the exception of the index files, each of the 351 files of a
GenBank release begins with the same header, except for the first line,
which contains the file name, and the sixth line, which contains the
title of the file. The first line of the file contains the file name
in character positions 1 to 9 and the full database name (Genetic Sequence
Data Bank) starting in column 22. The brief names of the files in this
release are listed in section 2.2.

  The second line contains the date of the current release in the form
`day month year', beginning in position 27. The fourth line contains
the current GenBank release number. The release number appears in
positions 48 to 52 and consists of three numbers separated by a decimal
point. The number to the left of the decimal is the major release
number. The digit to the right of the decimal indicates the version of
the major release; it is zero for the first version. The sixth line
contains a title for the file. The eighth line lists the number of
entries (loci), number of bases (or base pairs), and number of reports
of sequences (equal to number of entries in this case). These numbers are
right-justified at fixed positions. The number of entries appears in
positions 1 to 8, the number of bases in positions 16 to 26, and the
number of reports in positions 40 to 47. The third, fifth, seventh, and
ninth lines are blank.

1       10        20        30        40        50        60        70       79
---------+---------+---------+---------+---------+---------+---------+---------
GBBCT1.SEQ           Genetic Sequence Data Bank
                          15 April 2002

                NCBI-GenBank Flat File Release 131.0

                        Bacterial Sequences (Part 1)

   37811 loci,    97585608 bases, from    37811 reported sequences

---------+---------+---------+---------+---------+---------+---------+---------
1       10        20        30        40        50        60        70       79

Example 1. Sample File Header


3.2 Directory Files

3.2.1 Short Directory File

  The short directory file contains brief descriptions of all of the
sequence entries contained in this release. These descriptions are in
fifteen groups, one group for each of the fifteen sequence entry
data files. The first record at the beginning of a group of entries
contains the name of the group in uppercase characters, beginning in
position 21. The organism groups are PRIMATE, RODENT, OTHER MAMMAL,
OTHER VERTEBRATE, INVERTEBRATE, PLANT, BACTERIAL, STRUCTURAL RNA, VIRAL,
PHAGE, SYNTHETIC, UNANNOTATED, EXPRESSED SEQUENCE TAG, PATENT, or
SEQUENCE TAGGED SITE.  The second record is blank.

  Each record in the short directory contains the sequence entry name
(LOCUS) in the first 12 positions, followed by a brief definition of
the sequence beginning in column 13. The definition is truncated (at
the end of a word) to leave room at the right margin for at least one
space, the sequence length, and the letters `bp'. The length of the
sequence is printed right-justified to column 77, followed by the
letters `bp' in columns 78 and 79. The next-to-last record for a group
has `ZZZZZZZZZZ' in its first ten positions (where the entry name
would normally appear). The last record is a blank line. An example of
the short directory file format, showing the descriptions of the last
entries in the Other Vertebrate sequence data file and the first
entries of the Invertebrate sequence data file, is reproduced below:

1       10        20        30        40        50        60        70       79
---------+---------+---------+---------+---------+---------+---------+---------
ZEFWNT1G3   B.rerio wnt-1 gene (exon 3) for wnt-1 protein.                266bp
ZEFWNT1G4   B.rerio wnt-1 gene (exon 4) for wnt-1 protein.                647bp
ZEFZF54     Zebrafish homeotic gene ZF-54.                                246bp
ZEFZFEN     Zebrafish engrailed-like homeobox sequence.                   327bp
ZZZZZZZZZZ
 
                    INVERTEBRATE

AAHAV33A    Acanthocheilonema viteae pepsin-inhibitor-like-protein       1048bp
ACAAC01     Acanthamoeba castelani gene encoding actin I.                1571bp
ACAACTPH    Acanthamoeba castellanii actophorin mRNA, complete cds.       671bp
ACAMHCA     A.castellanii non-muscle myosin heavy chain gene, partial    5894bp
---------+---------+---------+---------+---------+---------+---------+---------
1       10        20        30        40        50        60        70       79
Example 2. Short Directory File


3.3 Index Files

There are six files containing indices to the entries in this release:

  Accession number index file (Accession and Version)
  Secondary accession number index file
  Keyword phrase index file
  Author name index file
  Journal citation index file
  Gene name index file

  The index keys (accession numbers, keywords, authors, journals, and
gene symbols.) of an index are sorted alphabetically. All index keys
appear in uppercase characters even though they appear in mixed case
in the sequence entries. Following each index key, the identifiers of the
sequence entries containing that key are listed (LOCUS name,
division abbreviation, and primary accession number). The division
abbreviations are:

 1. PRI - primate sequences
 2. ROD - rodent sequences
 3. MAM - other mammalian sequences
 4. VRT - other vertebrate sequences
 5. INV - invertebrate sequences
 6. PLN - plant, fungal, and algal sequences
 7. BCT - bacterial sequences
 8. VRL - viral sequences
 9. PHG - bacteriophage sequences
10. SYN - synthetic sequences
11. UNA - unannotated sequences
12. EST - EST sequences (expressed sequence tags) 
13. PAT - patent sequences
14. STS - STS sequences (sequence tagged sites) 
15. GSS - GSS sequences (genome survey sequences) 
16. HTG - HTGS sequences (high throughput genomic sequences) 
17. HTC - HTC sequences (high throughput cDNA sequences) 

  A line-oriented, TAB-delimited format is utilized for the gbaut.idx,
gbgen.idx,  gbjou.idx, gbkey.idx, and gbsec.idx indexes. Each index
key is presented on its own line, and is followed by a
LOCUS/Division/Accession triplet for every record containing the key:

Indexed-Term 
        LOCUS-name1 Div-code1 Accession1 
        LOCUS-name2 Div-code2 Accession2 
        LOCUS-name3 Div-code3 Accession3 
        .... 

  Here is an example of the format, in which TAB characters are displayed 
as ^I, and carriage-returns/newlines as $ : 

(H+,K+)-ATPASE BETA-SUBUNIT$ 
^IRATHKATPB^IROD^IM55655$ 
^IMUSATP4B1^IROD^IM64685$ 
^IMUSATP4B2^IROD^IM64686$ 
^IMUSATP4B3^IROD^IM64687$ 
^IMUSATP4B4^IROD^IM64688$ 
^IDOGATPASEB^IMAM^IM76486$ 

When viewed by a file browser such as 'less' or 'more' : 

(H+,K+)-ATPASE BETA-SUBUNIT 
        RATHKATPB ROD M55655 
        MUSATP4B1 ROD M64685 
        MUSATP4B2 ROD M64686 
        MUSATP4B3 ROD M64687 
        MUSATP4B4 ROD M64688 
        DOGATPASEB MAM M76486 

  Note that the index keys can be distinguished from LOCUS/DIV/ACCESSION 
by the fact that they do not start with a TAB character. So one can 
extract just the terms via simple text-processing: 

        perl -ne 'print unless /^\s+/' < gbkey.idx > terms.gbkey

  The format of the primary accession number index file is slightly
different, with each indexed key (Accession.Version) present on
the same line as the LOCUS/Division/Accession triplet:

Accession1.Version1 Locus-name1 Div-code1 Accession1 
Accession2.Version2 Locus-name2 Div-code2 Accession2 
.... 

  Here is an example of the format, in which TAB characters are displayed 
as ^I, and carriage-returns/newlines as $ : 

AC000102.1^IAC000102^IPRI^IAC000102$ 
AC000103.1^IAC000103^IPLN^IAC000103$ 
AC000104.1^IF19P19^IPLN^IAC000104$ 
AC000105.40^IAC000105^IPRI^IAC000105$ 
AC000106.1^IF7G19^IPLN^IAC000106$ 
AC000107.1^IAC000107^IPLN^IAC000107$ 
AC000108.1^IAC000108^IBCT^IAC000108$ 
AC000109.1^IHSAC000109^IPRI^IAC000109$ 
AC000110.1^IHSAC000110^IPRI^IAC000110$ 

When viewed by a file browser such as 'less' or 'more' : 

AC000102.1 AC000102 PRI AC000102 
AC000103.1 AC000103 PLN AC000103 
AC000104.1 F19P19 PLN AC000104 
AC000105.40 AC000105 PRI AC000105 
AC000106.1 F7G19 PLN AC000106 
AC000107.1 AC000107 PLN AC000107 
AC000108.1 AC000108 BCT AC000108 
AC000109.1 HSAC000109 PRI AC000109 
AC000110.1 HSAC000110 PRI AC000110 

3.3.1 Accession Number Index File - gbacc.idx

  Accession numbers are unique six character or eight-character alphanumeric
identifiers of GenBank database entries. The six-character accession
number format consists of a single uppercase letter, followed by 5 digits.
The eight-character accession number format consists of two uppercase
letters, followed by 6 digits.  Accessions provide an unchanging identifier
for the data with which they are associated, and we encourage you to cite
accession numbers whenever you refer to data from GenBank.

  GenBank entries can have both 'primary' and 'secondary' accessions
associated with them (see Section 3.5.6). Only primary accessions are present
in the gbacc.idx index.

3.3.2 Keyword Phrase Index File - gbkey.idx

  Keyword phrases consist of names for gene products and other
characteristics of sequence entries.

3.3.3 Author Name Index File - gbaut*.idx

The author name index files list all of the author names that appear
in the references within sequence records.

3.3.4 Journal Citation Index File - gbjou.idx

  The journal citation index file lists all of the citations that appear
in the references within sequence records.. All citations are truncated
to 80 characters.

3.3.5 Gene Name Index - gbgen.idx

  The /gene qualifiers of many GenBank entries contain values other than
official gene symbols, such as the product or the standard name of the gene.
Hence, NCBI has chosen to build an index (gbgen.idx) more like a keyword index
for this field, using both the GenBank /gene qualifier and the 'Gene.locus'
fields from the NCBI internal database as keys.

3.4 Sequence Entry Files

  GenBank releases contain one or more sequence entry data files, one
for each "division" of GenBank.

3.4.1 File Organization

  Each of these files has the same format and consists of two parts:
header information (described in section 3.1) and sequence entries for
that division (described in the following sections).

3.4.2  Entry Organization

  In the second portion of a sequence entry file (containing the
sequence entries for that division), each record (line) consists of
two parts. The first part is found in positions 1 to 10 and may
contain:

1. A keyword, beginning in column 1 of the record (e.g., REFERENCE is
a keyword).

2. A subkeyword beginning in column 3, with columns 1 and 2 blank
(e.g., AUTHORS is a subkeyword of REFERENCE). Or a subkeyword beginning
in column 4, with columns 1, 2, and 3 blank (e.g., PUBMED is a
subkeyword of REFERENCE).

3. Blank characters, indicating that this record is a continuation of
the information under the keyword or subkeyword above it.

4. A code, beginning in column 6, indicating the nature of an entry
(feature key) in the FEATURES table; these codes are described in
Section 3.4.12.1 below.

5. A number, ending in column 9 of the record. This number occurs in
the portion of the entry describing the actual nucleotide sequence and
designates the numbering of sequence positions.

6. Two slashes (//) in positions 1 and 2, marking the end of an entry.

  The second part of each sequence entry record contains the information
appropriate to its keyword, in positions 13 to 80 for keywords and
positions 11 to 80 for the sequence.

  The following is a brief description of each entry field. Detailed
information about each field may be found in Sections 3.4.4 to 3.4.14.

LOCUS	- A short mnemonic name for the entry, chosen to suggest the
sequence's definition. Mandatory keyword/exactly one record.

DEFINITION	- A concise description of the sequence. Mandatory
keyword/one or more records.

ACCESSION	- The primary accession number is a unique, unchanging
code assigned to each entry. (Please use this code when citing
information from GenBank.) Mandatory keyword/one or more records.

VERSION		- A compound identifier consisting of the primary
accession number and a numeric version number associated with the
current version of the sequence data in the record. This is followed
by an integer key (a "GI") assigned to the sequence by NCBI.
Mandatory keyword/exactly one record.

NID		- An alternative method of presenting the NCBI GI
identifier (described above). The NID is obsolete and was removed
from the GenBank flatfile format in December 1999.

KEYWORDS	- Short phrases describing gene products and other
information about an entry. Mandatory keyword in all annotated
entries/one or more records.

SEGMENT	- Information on the order in which this entry appears in a
series of discontinuous sequences from the same molecule. Optional
keyword (only in segmented entries)/exactly one record.

SOURCE	- Common name of the organism or the name most frequently used
in the literature. Mandatory keyword in all annotated entries/one or
more records/includes one subkeyword.

   ORGANISM	- Formal scientific name of the organism (first line)
and taxonomic classification levels (second and subsequent lines).
Mandatory subkeyword in all annotated entries/two or more records.

REFERENCE	- Citations for all articles containing data reported
in this entry. Includes seven subkeywords and may repeat. Mandatory
keyword/one or more records.

   AUTHORS	- Lists the authors of the citation. Optional
subkeyword/one or more records.

   CONSRTM	- Lists the collective names of consortiums associated
with the citation (eg, International Human Genome Sequencing Consortium),
rather than individual author names. Optional subkeyword/one or more records.

   TITLE	- Full title of citation. Optional subkeyword (present
in all but unpublished citations)/one or more records.

   JOURNAL	- Lists the journal name, volume, year, and page
numbers of the citation. Mandatory subkeyword/one or more records.

   MEDLINE	- Provides the Medline unique identifier for a
citation. Optional subkeyword/one record.

    PUBMED 	- Provides the PubMed unique identifier for a
citation. Optional subkeyword/one record.

   REMARK	- Specifies the relevance of a citation to an
entry. Optional subkeyword/one or more records.

COMMENT	- Cross-references to other sequence entries, comparisons to
other collections, notes of changes in LOCUS names, and other remarks.
Optional keyword/one or more records/may include blank records.

FEATURES	- Table containing information on portions of the
sequence that code for proteins and RNA molecules and information on
experimentally determined sites of biological significance. Optional
keyword/one or more records.

BASE COUNT	- Summary of the number of occurrences of each base
code in the sequence. Mandatory keyword/exactly one record.

ORIGIN	- Specification of how the first base of the reported sequence
is operationally located within the genome. Where possible, this
includes its location within a larger genetic map. Mandatory
keyword/exactly one record.

	- The ORIGIN line is followed by sequence data (multiple records).

// 	- Entry termination symbol. Mandatory at the end of an
entry/exactly one record.

3.4.3 Sample Sequence Data File

  An example of a complete sequence entry file follows. (This example
has only two entries.) Note that in this example, as throughout the
data bank, numbers in square brackets indicate items in the REFERENCE
list. For example, in ACARR58S, [1] refers to the paper by Mackay, et
al.

1       10        20        30        40        50        60        70       79
---------+---------+---------+---------+---------+---------+---------+---------
GBSMP.SEQ          Genetic Sequence Data Bank
                         15 December 1992

                 GenBank Flat File Release 74.0

                     Structural RNA Sequences

      2 loci,       236 bases, from     2 reported sequences

LOCUS       AAURRA        118 bp ss-rRNA            RNA       16-JUN-1986
DEFINITION  A.auricula-judae (mushroom) 5S ribosomal RNA.
ACCESSION   K03160
VERSION     K03160.1  GI:173593
KEYWORDS    5S ribosomal RNA; ribosomal RNA.
SOURCE      A.auricula-judae (mushroom) ribosomal RNA.
  ORGANISM  Auricularia auricula-judae
            Eukaryota; Fungi; Eumycota; Basidiomycotina; Phragmobasidiomycetes;
            Heterobasidiomycetidae; Auriculariales; Auriculariaceae.
REFERENCE   1  (bases 1 to 118)
  AUTHORS   Huysmans,E., Dams,E., Vandenberghe,A. and De Wachter,R.
  TITLE     The nucleotide sequences of the 5S rRNAs of four mushrooms and
            their use in studying the phylogenetic position of basidiomycetes
            among the eukaryotes
  JOURNAL   Nucleic Acids Res. 11, 2871-2880 (1983)
FEATURES             Location/Qualifiers
     rRNA            1..118
                     /note="5S ribosomal RNA"
BASE COUNT       27 a     34 c     34 g     23 t
ORIGIN      5' end of mature rRNA.
        1 atccacggcc ataggactct gaaagcactg catcccgtcc gatctgcaaa gttaaccaga
       61 gtaccgccca gttagtacca cggtggggga ccacgcggga atcctgggtg ctgtggtt
//
LOCUS       ABCRRAA       118 bp ss-rRNA            RNA       15-SEP-1990
DEFINITION  Acetobacter sp. (strain MB 58) 5S ribosomal RNA, complete sequence.
ACCESSION   M34766
VERSION     M34766.1  GI:173603
KEYWORDS    5S ribosomal RNA.
SOURCE      Acetobacter sp. (strain MB 58) rRNA.
  ORGANISM  Acetobacter sp.
            Prokaryotae; Gracilicutes; Scotobacteria; Aerobic rods and cocci;
            Azotobacteraceae.
REFERENCE   1  (bases 1 to 118)
  AUTHORS   Bulygina,E.S., Galchenko,V.F., Govorukhina,N.I., Netrusov,A.I.,
            Nikitin,D.I., Trotsenko,Y.A. and Chumakov,K.M.
  TITLE     Taxonomic studies of methylotrophic bacteria by 5S ribosomal RNA
            sequencing
  JOURNAL   J. Gen. Microbiol. 136, 441-446 (1990)
FEATURES             Location/Qualifiers
     rRNA            1..118
                     /note="5S ribosomal RNA"
BASE COUNT       27 a     40 c     32 g     17 t      2 others
ORIGIN      
        1 gatctggtgg ccatggcggg agcaaatcag ccgatcccat cccgaactcg gccgtcaaat
       61 gccccagcgc ccatgatact ctgcctcaag gcacggaaaa gtcggtcgcc gccagayy
//
---------+---------+---------+---------+---------+---------+---------+---------
1       10        20        30        40        50        60        70       79

Example 9. Sample Sequence Data File


3.4.4 LOCUS Format

  The items of information contained in the LOCUS record are always
found in fixed positions. The locus name (or entry name), which is
always sixteen characters or less, begins in position 13. The locus name
is designed to help group entries with similar sequences: the first
three characters usually designate the organism; the fourth and fifth
characters can be used to show other group designations, such as gene
product; for segmented entries the last character is one of a series
of sequential integers.

  The number of bases or base pairs in the sequence ends in position 40.
The letters `bp' are in positions 42 to 43. Positions 45 to 47 provide
the number of strands of the sequence. Positions 48 to 53 indicate the
type of molecule sequenced. Topology of the molecule is indicated in
positions 56 to 63.

  GenBank sequence entries are divided among many different
'divisions'. Each entry's division is specified by a three-letter code
in positions 65 to 67. See Section 3.3 for an explanation of division
codes.

  Positions 69 to 79 of the record contain the date the entry was
entered or underwent any substantial revisions, such as the addition
of newly published data, in the form dd-MMM-yyyy.

The detailed format for the LOCUS line format is as follows:

Positions  Contents
---------  --------
01-05      'LOCUS'
06-12      spaces
13-28      Locus name
29-29      space
30-40      Length of sequence, right-justified
41-41      space
42-43      bp
44-44      space
45-47      spaces, ss- (single-stranded), ds- (double-stranded), or
           ms- (mixed-stranded)
48-53      NA, DNA, RNA, tRNA (transfer RNA), rRNA (ribosomal RNA), 
           mRNA (messenger RNA), uRNA (small nuclear RNA), snRNA,
           snoRNA. Left justified.
54-55      space
56-63      'linear' followed by two spaces, or 'circular'
64-64      space
65-67      The division code (see Section 3.3)
68-68      space
69-79      Date, in the form dd-MMM-yyyy (e.g., 15-MAR-1991)

  Although each of these data values can be found at column-specific
positions, we encourage those who parse the contents of the LOCUS
line to use a token-based approach. This will prevent the need for
software changes if the spacing of the data values ever has to be
modified.

3.4.5 DEFINITION Format

  The DEFINITION record gives a brief description of the sequence,
proceeding from general to specific. It starts with the common name of
the source organism, then gives the criteria by which this sequence is
distinguished from the remainder of the source genome, such as the
gene name and what it codes for, or the protein name and mRNA, or some
description of the sequence's function (if the sequence is
non-coding). If the sequence has a coding region, the description may
be followed by a completeness qualifier, such as cds (complete coding
sequence). There is no limit on the number of lines that may be part
of the DEFINITION.  The last line must end with a period.

3.4.5.1 DEFINITION Format for NLM Entries

  The DEFINITION line for entries derived from journal-scanning at the NLM is
an automatically generated descriptive summary that accompanies each DNA and
protein sequence. It contains information derived from fields in a database 
that summarize the most important attributes of the sequence.  The DEFINITION
lines are designed to supplement the accession number and the sequence itself
as a means of uniquely and completely specifying DNA and protein sequences. The
following are examples of NLM DEFINITION lines:

NADP-specific isocitrate dehydrogenase [swine, mRNA, 1 gene, 1585 nt]

94 kda fiber cell beaded-filament structural protein [rats, lens, mRNA
Partial, 1 gene, 1873 nt]

inhibin alpha {promoter and exons} [mice, Genomic, 1 gene, 1102 nt, segment
1 of 2]

cefEF, cefG=acetyl coenzyme A:deacetylcephalosporin C o-acetyltransferase
[Acremonium chrysogenum, Genomic, 2 genes, 2639 nt]

myogenic factor 3, qmf3=helix-loop-helix protein [Japanese quails,
embryo, Peptide Partial, 246 aa]


  The first part of the definition line contains information describing
the genes and proteins represented by the molecular sequences.  This can
be gene locus names, protein names and descriptions that replace or augment
actual names.  Gene and gene product are linked by "=".  Any special
identifying terms are presented within brackets, such as: {promoter},
{N-terminal}, {EC 2.13.2.4}, {alternatively spliced}, or {3' region}.

  The second part of the definition line is delimited by square brackets, '[]',
and provides details about the molecule type and length.  The biological
source, i.e., genus and species or common name as cited by the author.
Developmental stage, tissue type and strain are included if available.
The molecule types include: Genomic, mRNA, Peptide. and Other Genomic
Material. Genomic molecules are assumed to be partial sequence unless
"Complete" is specified, whereas mRNA and peptide molecules are assumed
to be complete unless "Partial" is noted.

3.4.6 ACCESSION Format

  This field contains a series of six-character and/or eight-character
identifiers called 'accession numbers'. The six-character accession
number format consists of a single uppercase letter, followed by 5 digits.
The eight-character accession number format consists of two uppercase
letters, followed by 6 digits. The 'primary', or first, of the accession
numbers occupies positions 13 to 18 (6-character format) or positions
13 to 20 (8-character format). Subsequent 'secondary' accession numbers
(if present) are separated from the primary, and from each other, by a
single space. In some cases, multiple lines of secondary accession
numbers might be present, starting at position 13.

  The primary accession number of a GenBank entry provides a stable identifier
for the biological object that the entry represents. Accessions do not change
when the underlying sequence data or associated features change.

  Secondary accession numbers arise for a number of reasons. For example, a
single accession number may initially be assigned to a sequence described in
a publication. If it is later discovered that the sequence must be entered
into the database as multiple entries, each entry would receive a new primary
accession number, and the original accession number would appear as a secondary
accession number on each of the new entries.

3.4.7 VERSION Format

  This line contains two types of identifiers for a GenBank database entry:
a compound accession number and an NCBI GI identifier. 

LOCUS       AF181452     1294 bp    DNA             PLN       12-OCT-1999
DEFINITION  Hordeum vulgare dehydrin (Dhn2) gene, complete cds.
ACCESSION   AF181452
VERSION     AF181452.1  GI:6017929
            ^^^^^^^^^^  ^^^^^^^^^^
            Compound    NCBI GI
            Accession   Identifier
            Number

  A compound accession number consists of two parts: a stable, unchanging
primary-accession number portion (see Section 3.4.6 for a description of
accession numbers), and a sequentially increasing numeric version number.
The accession and version numbers are separated by a period. The initial
version number assigned to a new sequence is one. Compound accessions are
often referred to as "Accession.Version" .

  An accession number allows one to retrieve the same biological object in the
database, regardless of any changes that are made to the entry over time. But
those changes can include changes to the sequence data itself, which is of
fundamental importance to many database users. So a numeric version number is
associated with the sequence data in every database entry. If an entry (for
example, AF181452) undergoes two sequence changes, its compound accession
number on the VERSION line would start as AF181452.1 . After the first sequence
change this would become: AF181452.2 . And after the second change: AF181452.3 .

  The NCBI GI identifier of the VERSION line also serves as a method for
identifying the sequence data that has existed for a database entry over
time. GI identifiers are numeric values of one or more digits. Since they
are integer keys, they are less human-friendly than the Accession.Version
system described above. Returning to our example for AF181452, it was
initially assigned GI 6017929. If the sequence changes, a new integer GI will
be assigned, perhaps 7345003 . And after the second sequence change, perhaps
the GI would become 10456892 .

  Why are both these methods for identifying the version of the sequence
associated with a database entry in use? For two reasons:

- Some data sources processed by NCBI for incorporation into its Entrez
  sequence retrieval system do not version their own sequences.

- GIs provide a uniform, integer identifier system for every sequence
  NCBI has processed. Some products and systems derived from (or reliant
  upon) NCBI products and services prefer to use these integer identifiers
  because they can all be processed in the same manner.

GenBank Releases contain only the most recent versions of all sequences
in the database. However, older versions can be obtained via GI-based or
Accession.Version-based queries with NCBI's web-Entrez and network-Entrez
applications. A sequence revision history web page is also available:

	  http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/htbin-post/Entrez/girevhist

NOTE: All the version numbers for the compound Accession.Version identifier
system were initialized to a value of one in February 1999, when that
system was introduced.

3.4.8 KEYWORDS Format

  The KEYWORDS field does not appear in unannotated entries, but is
required in all annotated entries. Keywords are separated by
semicolons; a "keyword" may be a single word or a phrase consisting of
several words. Each line in the keywords field ends in a semicolon;
the last line ends with a period. If no keywords are included in the
entry, the KEYWORDS record contains only a period.

3.4.9 SEGMENT Format

  The SEGMENT keyword is used when two (or more) entries of known
relative orientation are separated by a short (<10 kb) stretch of DNA.
It is limited to one line of the form `n of m', where `n' is the
segment number of the current entry and `m' is the total number of
segments.

3.4.10 SOURCE Format

  The SOURCE field consists of two parts. The first part is found after
the SOURCE keyword and contains free-format information including an
abbreviated form of the organism name followed by a molecule type;
multiple lines are allowed, but the last line must end with a period.
The second part consists of information found after the ORGANISM
subkeyword. The formal scientific name for the source organism (genus
and species, where appropriate) is found on the same line as ORGANISM.
The records following the ORGANISM line list the taxonomic
classification levels, separated by semicolons and ending with a
period.

3.4.11 REFERENCE Format

  The REFERENCE field consists of five parts: the keyword REFERENCE, and
the subkeywords AUTHORS, TITLE (optional), JOURNAL, MEDLINE (optional),
PUBMED (optional), and REMARK (optional).

  The REFERENCE line contains the number of the particular reference and
(in parentheses) the range of bases in the sequence entry reported in
this citation. Additional prose notes may also be found within the
parentheses. The numbering of the references does not reflect
publication dates or priorities.

  The AUTHORS line lists the authors in the order in which they appear
in the cited article. Last names are separated from initials by a
comma (no space); there is no comma before the final `and'. The list
of authors ends with a period.  The TITLE line is an optional field,
although it appears in the majority of entries. It does not appear in
unpublished sequence data entries that have been deposited directly
into the GenBank data bank, the EMBL Nucleotide Sequence Data Library,
or the DNA Data Bank of Japan. The TITLE field does not end with a
period.

  The JOURNAL line gives the appropriate literature citation for the
sequence in the entry. The word `Unpublished' will appear after the
JOURNAL subkeyword if the data did not appear in the scientific
literature, but was directly deposited into the data bank. For
published sequences the JOURNAL line gives the Thesis, Journal, or
Book citation, including the year of publication, the specific
citation, or In press.

  The MEDLINE line provides the National Library of Medicine's Medline
unique identifier for a citation (if known). Medline UIs are 8 digit
numbers.

  The PUBMED line provides the PubMed unique identifier for a citation
(if known). PUBMED ids are numeric, and are record identifiers for article
abstracts in the PubMed database :

       http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/entrez/query.fcgi?db=PubMed

  Citations in PubMed that do not fall within Medline's scope will have only
a PUBMED identifier. Similarly, citations that *are* in Medline's scope but
which have not yet been assigned Medline UIs will have only a PUBMED identifier.
If a citation is present in both the PubMed and Medline databases, both a
MEDLINE and a PUBMED line will be present.

  The REMARK line is a textual comment that specifies the relevance
of the citation to the entry.

3.4.12 FEATURES Format

  GenBank releases use a feature table format designed jointly by
GenBank, the EMBL Nucleotide Sequence Data Library, and the DNA Data
Bank of Japan. This format is in use by all three databases. The
most complete and accurate Feature Table documentation can be found
on the Web at:

	http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/collab/FT/index.html

  Any discrepancy between the abbreviated feature table description
of these release notes and the complete documentation on the Web
should be resolved in favor of the version at the above URL.

  The Feature Table specification is also available as a printed
document: `The DDBJ/EMBL/GenBank Feature Table: Definition'. Contact
GenBank at the address shown on the first page of these Release Notes
if you would like a copy.

  The feature table contains information about genes and gene products,
as well as regions of biological significance reported in the
sequence. The feature table contains information on regions of the
sequence that code for proteins and RNA molecules. It also enumerates
differences between different reports of the same sequence, and
provides cross-references to other data collections, as described in
more detail below.

  The first line of the feature table is a header that includes the
keyword `FEATURES' and the column header `Location/Qualifier.' Each
feature consists of a descriptor line containing a feature key and a
location (see sections below for details). If the location does not
fit on this line, a continuation line may follow. If further
information about the feature is required, one or more lines
containing feature qualifiers may follow the descriptor line.

  The feature key begins in column 6 and may be no more than 15
characters in length. The location begins in column 22. Feature
qualifiers begin on subsequent lines at column 22. Location,
qualifier, and continuation lines may extend from column 22 to 80.

  Feature tables are required, due to the mandatory presence of the
source feature. The sections below provide a brief introduction to
the feature table format.

3.4.12.1 Feature Key Names

  The first column of the feature descriptor line contains the feature
key. It starts at column 6 and can continue to column 20. The list of
valid feature keys is shown below.

  Remember, the most definitive documentation for the feature table can
be found at:

	http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/collab/FT/index.html

allele		Obsolete; see variation feature key
attenuator	Sequence related to transcription termination
C_region	Span of the C immunological feature
CAAT_signal	`CAAT box' in eukaryotic promoters
CDS		Sequence coding for amino acids in protein (includes
		stop codon)
conflict	Independent sequence determinations differ
D-loop      	Displacement loop
D_segment	Span of the D immunological feature
enhancer	Cis-acting enhancer of promoter function
exon		Region that codes for part of spliced mRNA
gene            Region that defines a functional gene, possibly
                including upstream (promotor, enhancer, etc)
		and downstream control elements, and for which
		a name has been assigned.
GC_signal	`GC box' in eukaryotic promoters
iDNA		Intervening DNA eliminated by recombination
intron		Transcribed region excised by mRNA splicing
J_region	Span of the J immunological feature
LTR		Long terminal repeat
mat_peptide	Mature peptide coding region (does not include stop codon)
misc_binding	Miscellaneous binding site
misc_difference	Miscellaneous difference feature
misc_feature	Region of biological significance that cannot be described
		by any other feature
misc_recomb	Miscellaneous recombination feature
misc_RNA	Miscellaneous transcript feature not defined by other RNA keys
misc_signal	Miscellaneous signal
misc_structure	Miscellaneous DNA or RNA structure
modified_base	The indicated base is a modified nucleotide
mRNA		Messenger RNA
mutation 	Obsolete: see variation feature key
N_region	Span of the N immunological feature
old_sequence	Presented sequence revises a previous version
polyA_signal	Signal for cleavage & polyadenylation
polyA_site	Site at which polyadenine is added to mRNA
precursor_RNA	Any RNA species that is not yet the mature RNA product
prim_transcript	Primary (unprocessed) transcript
primer		Primer binding region used with PCR
primer_bind	Non-covalent primer binding site
promoter	A region involved in transcription initiation
protein_bind	Non-covalent protein binding site on DNA or RNA
RBS		Ribosome binding site
rep_origin	Replication origin for duplex DNA
repeat_region	Sequence containing repeated subsequences
repeat_unit	One repeated unit of a repeat_region
rRNA		Ribosomal RNA
S_region	Span of the S immunological feature
satellite	Satellite repeated sequence
scRNA		Small cytoplasmic RNA
sig_peptide	Signal peptide coding region
snRNA		Small nuclear RNA
source		Biological source of the sequence data represented by
		a GenBank record. Mandatory feature, one or more per record.
		For organisms that have been incorporated within the
		NCBI taxonomy database, an associated /db_xref="taxon:NNNN"
		qualifier will be present (where NNNNN is the numeric
		identifier assigned to the organism within the NCBI taxonomy
		database).
stem_loop	Hair-pin loop structure in DNA or RNA
STS		Sequence Tagged Site; operationally unique sequence that
		identifies the combination of primer spans used in a PCR assay
TATA_signal	`TATA box' in eukaryotic promoters
terminator	Sequence causing transcription termination
transit_peptide	Transit peptide coding region
transposon	Transposable element (TN)
tRNA 		Transfer RNA
unsure		Authors are unsure about the sequence in this region
V_region	Span of the V immunological feature
variation 	A related population contains stable mutation
- (hyphen)	Placeholder
-10_signal	`Pribnow box' in prokaryotic promoters
-35_signal	`-35 box' in prokaryotic promoters
3'clip		3'-most region of a precursor transcript removed in processing
3'UTR		3' untranslated region (trailer)
5'clip		5'-most region of a precursor transcript removed in processing
5'UTR		5' untranslated region (leader)


3.4.12.2 Feature Location

  The second column of the feature descriptor line designates the
location of the feature in the sequence. The location descriptor
begins at position 22. Several conventions are used to indicate
sequence location.

  Base numbers in location descriptors refer to numbering in the entry,
which is not necessarily the same as the numbering scheme used in the
published report. The first base in the presented sequence is numbered
base 1. Sequences are presented in the 5 to 3 direction.

Location descriptors can be one of the following:

1. A single base;

2. A contiguous span of bases;

3. A site between two bases;

4. A single base chosen from a range of bases;

5. A single base chosen from among two or more specified bases;

6. A joining of sequence spans;

7. A reference to an entry other than the one to which the feature
belongs (i.e., a remote entry), followed by a location descriptor
referring to the remote sequence;

  A site between two residues, such as an endonuclease cleavage site, is
indicated by listing the two bases separated by a carat (e.g., 23^24).

  A single residue chosen from a range of residues is indicated by the
number of the first and last bases in the range separated by a single
period (e.g., 23.79). The symbols < and > indicate that the end point
of the range is beyond the specified base number.

  A contiguous span of bases is indicated by the number of the first and
last bases in the range separated by two periods (e.g., 23..79). The
symbols < and > indicate that the end point of the range is beyond the
specified base number. Starting and ending positions can be indicated
by base number or by one of the operators described below.

  Operators are prefixes that specify what must be done to the indicated
sequence to locate the feature. The following are the operators
available, along with their most common format and a description.

complement (location): The feature is complementary to the location
indicated. Complementary strands are read 5 to 3.

join (location, location, .. location): The indicated elements should
be placed end to end to form one contiguous sequence.

order (location, location, .. location): The elements are found in the
specified order in the 5 to 3 direction, but nothing is implied about
the rationality of joining them.

3.4.12.3  Feature Qualifiers

  Qualifiers provide additional information about features. They take
the form of a slash (/) followed by a qualifier name and, if
applicable, an equal sign (=) and a qualifier value. Feature
qualifiers begin at column 22.

Qualifiers convey many types of information. Their values can,
therefore, take several forms:

1. Free text;
2. Controlled vocabulary or enumerated values;
3. Citations or reference numbers;
4. Sequences;
5. Feature labels.

  Text qualifier values must be enclosed in double quotation marks. The
text can consist of any printable characters (ASCII values 32-126
decimal). If the text string includes double quotation marks, each set
must be `escaped' by placing a double quotation mark in front of it
(e.g., /note="This is an example of ""escaped"" quotation marks").

  Some qualifiers require values selected from a limited set of choices.
For example, the `/direction' qualifier has only three values `left,'
`right,' or `both.' These are called controlled vocabulary qualifier
values. Controlled qualifier values are not case sensitive; they can
be entered in any combination of upper- and lowercase without changing
their meaning.

  Citation or published reference numbers for the entry should be
enclosed in square brackets ([]) to distinguish them from other
numbers.

  A literal sequence of bases (e.g., "atgcatt") should be enclosed in
quotation marks. Literal sequences are distinguished from free text by
context. Qualifiers that take free text as their values do not take
literal sequences, and vice versa.

  The `/label=' qualifier takes a feature label as its qualifier.
Although feature labels are optional, they allow unambiguous
references to the feature. The feature label identifies a feature
within an entry; when combined with the accession number and the name
of the data bank from which it came, it is a unique tag for that
feature. Feature labels must be unique within an entry, but can be the
same as a feature label in another entry. Feature labels are not case
sensitive; they can be entered in any combination of upper-and
lowercase without changing their meaning.

The following is a partial list of feature qualifiers.

/anticodon	Location of the anticodon of tRNA and the amino acid
		for which it codes

/bound_moiety	Moiety bound

/citation	Reference to a citation providing the claim of or
		evidence for a feature

/codon		Specifies a codon that is different from any found in the
		reference genetic code

/codon_start	Indicates the first base of the first complete codon
		in a CDS (as 1 or 2 or 3)

/cons_splice	Identifies intron splice sites that do not conform to
		the 5'-GT... AG-3' splice site consensus

/db_xref	A database cross-reference; pointer to related information
		in another database. A description of all cross-references
		can be found at:

		http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/collab/db_xref.html

/direction	Direction of DNA replication

/EC_number	Enzyme Commission number for the enzyme product of the
		sequence

/evidence	Value indicating the nature of supporting evidence

/frequency	Frequency of the occurrence of a feature

/function	Function attributed to a sequence

/gene		Symbol of the gene corresponding to a sequence region (usable
		with all features)

/label		A label used to permanently identify a feature

/map		Map position of the feature in free-format text

/mod_base	Abbreviation for a modified nucleotide base

/note		Any comment or additional information

/number		A number indicating the order of genetic elements
		(e.g., exons or introns) in the 5 to 3 direction

/organism	Name of the organism that is the source of the
		sequence data in the record. 

/partial	Differentiates between complete regions and partial ones

/phenotype	Phenotype conferred by the feature

/product	Name of a product encoded by a coding region (CDS)
		feature

/pseudo		Indicates that this feature is a non-functional
		version of the element named by the feature key

/rpt_family	Type of repeated sequence; Alu or Kpn, for example

/rpt_type	Organization of repeated sequence

/rpt_unit	Identity of repeat unit that constitutes a repeat_region

/standard_name	Accepted standard name for this feature

/transl_except	Translational exception: single codon, the translation
		of which does not conform to the reference genetic code

/translation	Amino acid translation of a coding region

/type		Name of a strain if different from that in the SOURCE field

/usedin		Indicates that feature is used in a compound feature
		in another entry

3.4.12.4 Cross-Reference Information

  One type of information in the feature table lists cross-references to
the annual compilation of transfer RNA sequences in Nucleic Acids
Research, which has kindly been sent to us on CD-ROM by Dr. Sprinzl.
Each tRNA entry of the feature table contains a /note= qualifier that
includes a reference such as `(NAR: 1234)' to identify code 1234 in
the NAR compilation. When such a cross-reference appears in an entry
that contains a gene coding for a transfer RNA molecule, it refers to
the code in the tRNA gene compilation. Similar cross-references in
entries containing mature transfer RNA sequences refer to the
companion compilation of tRNA sequences published by D.H. Gauss and M.
Sprinzl in Nucleic Acids Research.

3.4.12.5 Feature Table Examples

  In the first example a number of key names, feature locations, and
qualifiers are illustrated, taken from different sequences. The first
table entry is a coding region consisting of a simple span of bases
and including a /gene qualifier. In the second table entry, an NAR
cross-reference is given (see the previous section for a discussion of
these cross-references). The third and fourth table entries use the
symbols `<`and `>' to indicate that the beginning or end of the
feature is beyond the range of the presented sequence. In the fifth
table entry, the symbol `^' indicates that the feature is between
bases.

1       10        20        30        40        50        60        70       79
---------+---------+---------+---------+---------+---------+---------+---------
     CDS             5..1261
                     /product="alpha-1-antitrypsin precursor"
                     /map="14q32.1"
                     /gene="PI"
     tRNA            1..87
                     /note="Leu-tRNA-CAA (NAR: 1057)"
                     /anticodon=(pos:35..37,aa:Leu)
     mRNA            1..>66
                     /note="alpha-1-acid glycoprotein mRNA"
     transposon      <1..267
                     /note="insertion element IS5"
     misc_recomb     105^106
                     /note="B.subtilis DNA end/IS5 DNA start"
     conflict        258
                     /replace="t"
                     /citation=[2]
---------+---------+---------+---------+---------+---------+---------+---------
1       10        20        30        40        50        60        70       79

Example 10. Feature Table Entries


The next example shows the representation for a CDS that spans more
than one entry.

1       10        20        30        40        50        60        70       79
---------+---------+---------+---------+---------+---------+---------+---------
LOCUS       HUMPGAMM1    3688 bp ds-DNA             PRI       15-OCT-1990
DEFINITION  Human phosphoglycerate mutase (muscle specific isozyme) (PGAM-M)
            gene, 5' end.
ACCESSION   M55673 M25818 M27095
KEYWORDS    phosphoglycerate mutase.
SEGMENT     1 of 2
  .
  .
  .
FEATURES             Location/Qualifiers
     CAAT_signal     1751..1755
                     /gene="PGAM-M"
     TATA_signal     1791..1799
                     /gene="PGAM-M"
     exon            1820..2274
                     /number=1
                     /EC_number="5.4.2.1"
                     /gene="PGAM-M"
     intron          2275..2377
                     /number=1
                     /gene="PGAM2"
     exon            2378..2558
                     /number=2
                     /gene="PGAM-M"
  .
  .
  .
//
LOCUS       HUMPGAMM2     677 bp ds-DNA             PRI       15-OCT-1990
DEFINITION  Human phosphoglycerate mutase (muscle specific isozyme) (PGAM-M),
            exon 3.
ACCESSION   M55674 M25818 M27096
KEYWORDS    phosphoglycerate mutase.
SEGMENT     2 of 2
  .
  .
  .
FEATURES             Location/Qualifiers
     exon            255..457
                     /number=3
                     /gene="PGAM-M"
     intron          order(M55673:2559..>3688,<1..254)
                     /number=2
                     /gene="PGAM-M"
     mRNA            join(M55673:1820..2274,M55673:2378..2558,255..457)
                     /gene="PGAM-M"
     CDS             join(M55673:1861..2274,M55673:2378..2558,255..421)
                     /note="muscle-specific isozyme"
                     /gene="PGAM2"
                     /product="phosphoglycerate mutase"
                     /codon_start=1
                     /translation="MATHRLVMVRHGESTWNQENRFCGWFDAELSEKGTEEAKRGAKA
                     IKDAKMEFDICYTSVLKRAIRTLWAILDGTDQMWLPVVRTWRLNERHYGGLTGLNKAE
                     TAAKHGEEQVKIWRRSFDIPPPPMDEKHPYYNSISKERRYAGLKPGELPTCESLKDTI
                     ARALPFWNEEIVPQIKAGKRVLIAAHGNSLRGIVKHLEGMSDQAIMELNLPTGIPIVY
                     ELNKELKPTKPMQFLGDEETVRKAMEAVAAQGKAK"
  .
  .
  .
//
---------+---------+---------+---------+---------+---------+---------+---------
1       10        20        30        40        50        60        70       79

Example 11. Joining Sequences


3.4.13 ORIGIN Format

  The ORIGIN record may be left blank, may appear as `Unreported.' or
may give a local pointer to the sequence start, usually involving an
experimentally determined restriction cleavage site or the genetic
locus (if available). The ORIGIN record ends in a period if it
contains data, but does not include the period if the record is left
empty (in contrast to the KEYWORDS field which contains a period
rather than being left blank).

3.4.14 SEQUENCE Format

  The nucleotide sequence for an entry is found in the records following
the ORIGIN record. The sequence is reported in the 5 to 3 direction.
There are sixty bases per record, listed in groups of ten bases
followed by a blank, starting at position 11 of each record. The
number of the first nucleotide in the record is given in columns 4 to
9 (right justified) of the record.


4. ALTERNATE RELEASES

  NCBI is supplying sequence data in the GenBank flat file format to
maintain compatibility with existing software which require that
particular format.  Although we have made every effort to ensure
that these data are presented in the traditional flat file format,
if you encounter any problems in using these data with software which
is based upon the flat file format, please contact us at:

              info@ncbi.nlm.nih.gov

  The flat file is just one of many possible report formats that can be
generated from the richer representation supported by the ASN.1 form of the
data.  Developers of new software tools should consider using the ASN.1 form
directly to take advantage of those features.  Documentation and a Software
Developer's Toolkit for ASN.1 are available through NCBI.  You may call NCBI
at (301)496-2475, or subscribe to a developers' electronic newsgroup by
sending your name, address, affiliation, and e-mail address to:

              bits-request@ncbi.nlm.nih.gov

  The Software Developer's Toolkit and PostScript documentation for UNIX,
VMS, Ultrix, AIX, MacOS, DOS, and Microsoft Windows systems is available
in a compressed UNIX tar file by anonymous ftp from 'ftp.ncbi.nih.gov',
in the toolbox/ncbi_tools directory. The file is 'ncbi.tar.Z'.


5. KNOWN PROBLEMS OF THE GENBANK DATABASE

5.1 Incorrect Gene Symbols in Entries and Index

  The /gene qualifier for many GenBank entries contains values other than the
official gene symbol, such as the product or the standard name of the gene. The
gene symbol index (gbgen.idx) is created from the data in the /gene qualifier
and therefore may contain data other than official gene symbols.


6. GENBANK ADMINISTRATION 

  The National Center for Biotechnology Information (NCBI), National Library
of Medicine, National Institutes of Health, is responsible for the production
and distribution of the NIH GenBank Sequence Database.  NCBI distributes
GenBank sequence data by anonymous FTP, e-mail servers and other
network services.  For more information, you may contact NCBI at the
e-mail address:  info@ncbi.nlm.nih.gov  or by phone: 301-496-2475.

6.1 Registered Trademark Notice

  GenBank (R) is a registered trademark of the U.S. Department of Health
and Human Services for the Genetic Sequence Data Bank.

6.2 Citing GenBank

  If you have used GenBank in your research, we would appreciate it if
you would include a reference to GenBank in all publications related
to that research.

  When citing data in GenBank, it is appropriate to give the sequence
name, primary accession number, and the publication in which the
sequence first appeared.  If the data are unpublished, we urge you to
contact the group which submitted the data to GenBank to see if there
is a recent publication or if they have determined any revisions or
extensions of the data.

  It is also appropriate to list a reference for GenBank itself.  The
following publication, which describes the GenBank database, should
be cited:

    Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Rapp B.A., 
    Wheeler D.L.  GenBank. Nucl. Acids Res. 28(1):15-18 (2000)

  The following statement is an example of how you may cite GenBank
data.  It cites the sequence, its primary accession number, the group
who determined the sequence, and GenBank.  The numbers in parentheses
refer to the GenBank citation above and to the REFERENCE in the
GenBank sequence entry.

`We scanned the GenBank (1) database for sequence similarities and
found one sequence (2), GenBank accession number J01016, which showed
significant similarity...'

  (1) Benson, D.A. et al. Nucl. Acids Res. 28(1):15-18 (2000)
  (2) Nellen, W. and Gallwitz, D. J. Mol. Biol. 159, 1-18 (1982)

6.3 GenBank Distribution Formats and Media

  Complete flat file releases of the GenBank database are available via
NCBI's anonymous ftp server:

	ftp://ftp.ncbi.nih.gov

  Each release is cumulative, incorporating all previous GenBank data.
No retrieval software is provided. GenBank distribution via CD-ROM
ceased as of GenBank Release 106.0 (April, 1998).

  Mirrors of the GenBank FTP site at the NCBI are available from the
San Diego Supercomputer Center and the University of Indiana:

	ftp://genbank.sdsc.edu/pub
	ftp://bio-mirror.net/biomirror/genbank/

6.4 Other Methods of Accessing GenBank Data

  Entrez is a molecular biology database system that presents an integrated
view of DNA and protein sequence data, 3D structure data, complete genomes,
and associated MEDLINE entries. The system is produced by the National
Center for Biotechnology Information (NCBI), and is available only via
the Internet (using the Web-Entrez and Network-Entrez applications).

  Accessing Entrez is easy: if you have a World Wide Web browser, such as
Netscape or Internet-Explorer, simply point your browser to:

	 http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/

  The Web version of Entrez has all the capabilities of the network version,
but with the visual style of the World Wide Web. If you prefer the "look and
feel" of Network-Entrez, you may download Network-Entrez from the NCBI's
FTP server:

	ftp://ftp.ncbi.nih.gov/

Versions are available for PC/Windows, Macintosh and several Unix variants.

  For information about Network-Entrez, Web-Entrez or any other NCBI
services, you may contact NCBI by e-mail at info@ncbi.nlm.nih.gov or by
phone at 301-496-2475.

6.5 Request for Corrections and Comments

  We welcome your suggestions for improvements to GenBank. We are
especially interested to learn of errors or inconsistencies in the
data.  BankIt or Sequin can be used to submit revisions to previous
submissions.  In addition, suggestions and corrections can be sent by
electronic mail to:  update@ncbi.nlm.nih.gov.  Please be certain to
indicate the GenBank release number (e.g., Release 131.0) and the
primary accession number of the entry to which your comments apply; it
is helpful if you also give the entry name and the current contents of
any data field for which you are recommending a change.

6.6  Credits and Acknowledgments

Credits -

GenBank Release Coordination	
	Mark Cavanaugh

GenBank Submission Coordination	
	Ilene Mizrachi

GenBank Annotation Staff
        Lori Black, Larissa Brown, Larry Chlumsky, Karen Clark, Irene Fang,
	Michael Fetchko, Anjanette Johnston, Pierre Ledoux, Richard McVeigh,
	Leonie Misquitta, Ilene Mizrachi, DeAnne Olsen Cravaritis,  
        Chris O'Sullivan, David Rasko, Leigh Riley, Gert Roosen, Susan 
        Schafer, Suh-suh Wang, Jane Weisemann, Steven Wilhite, and 
        Linda Yankie

Data Management and Preparation
	Vladimir Alekseyev, Serge Bazhin, Anton Butanaev, Mark Cavanaugh,
	Hsiu-Chuan Chen, Jonathan Kans, Michael Kimelman, Jim Ostell,
	Joel Plotkin, Karl Sirotkin, Vladimir Soussov, Elena Starchenko,
	Hanzhen Sun, Tatiana Tatusov, Carolyn Tolstoshev, Jane Weisemann,
	Eugene Yaschenko

Database Administration
	Helen Epting, Slava Khotomliansky, Tony Stearman

User Support
        Nancy Allmang, Medha Bhagwat, Peter Cooper, Susan Dombrowski, 
        Renata Geer, Dawn Lipshultz, Eugenia Posey-Marcos, Scott McGinnis,
        Vyvy Pham, Barbara Rapp, Monica Romiti, Tao Tao, Rose Marie Woodsmall, 		
	David Wheeler 

Project Direction
	David Lipman


Acknowledgments - 

  Contractor support for GenBank production and distribution has been
provided by Management Systems Designers, Inc., ComputerCraft Corporation,
and The KEVRIC Company, Inc.

6.7 Disclaimer

  The United States Government makes no representations or warranties
regarding the content or accuracy of the information.  The United States
Government also makes no representations or warranties of merchantability
or fitness for a particular purpose or that the use of the sequences will
not infringe any patent, copyright, trademark, or other rights.  The
United States Government accepts no responsibility for any consequence
of the receipt or use of the information.

  For additional information about GenBank releases, please contact
NCBI by e-mail at info@ncbi.nlm.nih.gov, by phone at (301) 496-2475,
or by mail at:

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