Release Notes For GenBank Release 123

GBREL.TXT          Genetic Sequence Data Bank
                         April 15 2001

               NCBI-GenBank Flat File Release 123.0

                    Distribution Release Notes

 11545572 loci, 12418544023 bases, from 11545572 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 123.0
1.2 Cutoff Date
1.3 Important Changes in Release 123.0
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 123.0

  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 123.0 is a release of sequence data by NCBI in the GenBank
flat file 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: ncbi.nlm.nih.gov .

1.2 Cutoff Date

  This full release, 123.0, incorporates data available to the databases as of
April 17, 2001.  For more recent data, users are advised to:

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

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

    A mirror of the GenBank FTP site at the NCBI is available from the San Diego
    Supercomputer Center:

	ftp://genbank.sdsc.edu/pub

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

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

  o Use the NCBI 'query' email server to search the GenBank Updates. Instructions
    regarding the use of the e-mail server can be obtained by sending an email
    message with the word 'help' in it to:  query@ncbi.nlm.nih.gov

1.3 Important Changes in Release 123.0

1.3.1 Headers missing for nine GSS files

  Some manual processing of GSS division files was required in order to
correct a content problem. This has resulted in the lack of the standard 
flatfile header (See Section 3.1) for nine of the GSS flatfiles:

  gbgss1.seq.gz
  gbgss2.seq.gz
  gbgss3.seq.gz
  gbgss4.seq.gz
  gbgss5.seq.gz
  gbgss6.seq.gz
  gbgss19.seq.gz
  gbgss36.seq.gz
  gbgss37.seq.gz

1.3.2 Organizational changes

  Due to database growth, the EST division is now being split into 111 pieces.

  Due to database growth, the GSS division is now being split into 37 pieces.

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

  Due to database growth, the PRI division is now being split into 10 pieces.

1.3.3 New HTC division introduced

  A new GenBank division for unfinished high-throughput cDNA sequencing (HTC)
is now included in GenBank releases. HTC sequences may have 5'UTR and 3'UTR at
their ends, partial coding regions, and introns. A keyword of "HTC" will be present,
in addition to division code "HTC". Those HTC sequences that undergo finishing
(eg, re-sequencing) will move to the appropriate taxonomic GenBank division and
the "HTC" keyword will be removed. A recent project that generates HTC-quality
data is described in:

	Hayashizaki, Y.
	Functional annotation of a full-length mouse cDNA collection
	Nature 409, 685-690 (2001)

1.3.4 Minor change to REFERENCE line

  The REFERENCE keyword for the literature citations associated with a GenBank
record has previously required a parenthetical component indicating either the
basepair span to which the citation applies, or "sites" for citations providing
annotation rather than sequence data. Here are some examples:

	REFERENCE   1  (bases 1 to 262290)
	REFERENCE   2  (sites)
	REFERENCE   3  (bases 1 to 456; bases 700 to 2334)

  As of GenBank Release 123.0 (April 2001), this component of the REFERENCE
line has been made optional, to simplify submissions involving a large number
of sequence changes when the submittor is unable to identify all the relevant
basepair spans.

  Users interested in the details of how a sequence has changed can use
NCBI's Blast-2-Sequences tool:

	http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/blast/bl2seq/bl2.html

1.4 Upcoming Changes

1.4.1 LOCUS line format change : to accomodate longer names and sequences

  When the LOCUS line format for the GenBank flatfile was designed nearly
two decades ago, sequences over 10 Mbp in length were not anticipated. As
a result, the maximum length of a LOCUS name is nine characters, and the
maximum length of a sequence is 9,999,999 bases :

---------+---------+---------+---------+---------+---------+---------+---------
1       10        20        30        40        50        60        70       79
LOCUS       AB000383     5423 bp    DNA   circular  VRL       05-FEB-1999

Positions  Contents
---------  --------
01-05      LOCUS
06-12      spaces
13-21      Locus name
22-22      space
23-29      Length of sequence, right-justified
31-32      bp
34-36      Blank, ss- (single-stranded), ds- (double-stranded), or
           ms- (mixed-stranded)
37-42      Blank, DNA, RNA, tRNA (transfer RNA), rRNA (ribosomal RNA), 
           mRNA (messenger RNA), uRNA (small nuclear RNA), snRNA
43-52      Blank (implies linear) or circular
53-55      The division code (see Section 3.3)
63-73      Date, in the form dd-MMM-yyyy (e.g., 15-MAR-1991)

  This leads to several problems: a) meaningful names of more than nine
characters cannot be utilized; b) the nine-character limit causes LOCUS
names to be truncated for many segmented sets of more than ten members
(see AF272557, AF272558, etc); c) invalid LOCUS lines result when the
GenBank flatfile format is used to display other types of sequence data.

  For (c), consider human contig Hs22_11677 derived from the sequences in
the HTG division of GenBank:

LOCUS       Hs22_1167722998459 bp    DNA            PRI       10-FEB-2001
DEFINITION  Homo sapiens chromosome 22 working draft sequence segment.
ACCESSION   NT_011520

  The LOCUS name ( Hs22_11677 ) collides with the sequence length ( 22998459 )
due to the restrictions of the LOCUS line format.

  To address the LOCUS problems, a new LOCUS line format which allows names
of up to 18 characters and sequences of up to 99,999,999,999 bases will be
utilized for all GenBank records starting with Release 126.0 in October 2001:

---------+---------+---------+---------+---------+---------+---------+---------
1       10        20        30        40        50        60        70       79
LOCUS       18_Char_LOCUS_Name 99999999999 bp ss-snRNA circular DIV DD-MMM-YYYY

Positions  Contents
---------  --------
01-05      LOCUS
06-12      spaces
13-30      Locus name
31-31      space
32-42      Length of sequence, right-justified
43-43      space
44-45      bp
46-46      space
47-49      Blank, ss- (single-stranded), ds- (double-stranded), or
           ms- (mixed-stranded)
50-54      Blank, DNA, RNA, tRNA (transfer RNA), rRNA (ribosomal RNA), 
           mRNA (messenger RNA), uRNA (small nuclear RNA), snRNA
55-55      space
56-63      Blank (implies linear) 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)

  Here's how an existing record would appear using this new format:

LOCUS       AB000383                  5423 bp    DNA   circular VRL 05-FEB-1999
DEFINITION  Leucania seperata nuclear polyhedrosis virus DNA for p13, xe,
            envelope protein, complete cds.
ACCESSION   AB000383

  Sample GenBank flatfiles with the new LOCUS line format will be made
available after Releases 124.0 (June) and 125.0 (August), so that developers
can test software that parses GenBank flatfiles. Further announcements about
the LOCUS line change will be made via these release notes and the GenBank
newsgroup (bionet.molbio.genbank).

1.4.2 NCBI's ftp address will be changed

  At some point in the near future NCBI's ftp address will be changed.
The current address:

	ncbi.nlm.nih.gov

will become:

	ftp.ncbi.nih.gov

  Additional details about this change will be made available via these
release notes and the GenBank newsgroup (bionet.molbio.genbank) as they
become available.

1.4.3 Selenocysteine representation

  Selenocysteine residues within the protein translations of coding
region features have been represented in GenBank via the letter 'X'
and a /transl_except qualifier. At the May 1999 DDBJ/EMBL/GenBank
collaborative meeting, it was learned that IUPAC plans to adopt the
letter 'U' for selenocysteine.

  DDBJ, EMBL, and GenBank will thus use this new amino acid abbreviation
for its /translation qualifiers. Although a timetable for its appearance
has not been finalized, we are mentioning this now because the introduction
of a new residue abbreviation is a fairly fundamental change.

  Details about the use of 'U' will be made available via these release
notes and the GenBank newsgroup as they become available.

1.4.4 New REFERENCE type for on-line journals

  Agreement was reached at the May 1999 collaborative DDBJ/EMBL/GenBank
meeting that an effort should be made to accomodate references which are
published only on-line. Until specifications for such references are
available from library organizations, GenBank will present them in a manner
like this:

	REFERENCE   1  (bases 1 to 2858)
	  AUTHORS   Smith, J.
	  TITLE     Cloning and expression of a phospholipase gene
	  JOURNAL   Online Publication
	  REMARK    Online-Journal-name; Article Identifier; URL

  This format is still tentative; additional information about this new
reference type will be made available via these release notes.

1.5 Request for Direct Submission of Sequence Data

  A successful GenBank requires that the 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 ncbi.nlm.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://ncbi.nlm.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 225 files. The list
that follows describes 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. gbjou.idx 	- Index of the entries according to journal citation.
15. gbgen.idx 	- Index of the entries according to gene names.
16. gbsec.idx	- Index of the entries according to secondary accession number.
17. gbpri1.seq 	- Primate sequence entries, part 1.
18. gbpri2.seq 	- Primate sequence entries, part 2.
19. gbpri3.seq 	- Primate sequence entries, part 3.
20. gbpri4.seq 	- Primate sequence entries, part 4.
21. gbpri5.seq 	- Primate sequence entries, part 5.
22. gbpri6.seq 	- Primate sequence entries, part 6.
23. gbpri7.seq 	- Primate sequence entries, part 7.
24. gbpri8.seq 	- Primate sequence entries, part 8.
25. gbpri9.seq 	- Primate sequence entries, part 9.
26. gbpri10.seq	- Primate sequence entries, part 10.
27. gbrod1.seq 	- Rodent sequence entries, part 1.
28. gbrod2.seq 	- Rodent sequence entries, part 2.
29. gbmam.seq 	- Other mammalian sequence entries.
30. gbvrt.seq 	- Other vertebrate sequence entries.
31. gbinv1.seq 	- Invertebrate sequence entries, part 1.
32. gbinv2.seq 	- Invertebrate sequence entries, part 2.
33. gbinv3.seq 	- Invertebrate sequence entries, part 3.
34. gbinv4.seq 	- Invertebrate sequence entries, part 4.
35. gbpln1.seq 	- Plant sequence entries (including fungi and algae), part 1.
36. gbpln2.seq 	- Plant sequence entries (including fungi and algae), part 2.
37. gbpln3.seq 	- Plant sequence entries (including fungi and algae), part 3.
38. gbpln4.seq 	- Plant sequence entries (including fungi and algae), part 4.
39. gbbct1.seq 	- Bacterial sequence entries, part 1.
40. gbbct2.seq 	- Bacterial sequence entries, part 2.
41. gbbct3.seq 	- Bacterial sequence entries, part 3.
42. gbvrl1.seq 	- Viral sequence entries, part 1.
43. gbvrl2.seq 	- Viral sequence entries, part 2.
44. gbphg.seq 	- Phage sequence entries.
45. gbsyn.seq 	- Synthetic and chimeric sequence entries.
46. gbuna.seq 	- Unannotated sequence entries.
47. gbest1.seq  - EST (expressed sequence tag) sequence entries, part 1.
48. gbest2.seq  - EST (expressed sequence tag) sequence entries, part 2.
49. gbest3.seq  - EST (expressed sequence tag) sequence entries, part 3.
50. gbest4.seq  - EST (expressed sequence tag) sequence entries, part 4.
51. gbest5.seq  - EST (expressed sequence tag) sequence entries, part 5.
52. gbest6.seq  - EST (expressed sequence tag) sequence entries, part 6.
53. gbest7.seq  - EST (expressed sequence tag) sequence entries, part 7.
54. gbest8.seq  - EST (expressed sequence tag) sequence entries, part 8.
55. gbest9.seq  - EST (expressed sequence tag) sequence entries, part 9.
56. gbest10.seq - EST (expressed sequence tag) sequence entries, part 10.
57. gbest11.seq - EST (expressed sequence tag) sequence entries, part 11.
58. gbest12.seq - EST (expressed sequence tag) sequence entries, part 12.
59. gbest13.seq - EST (expressed sequence tag) sequence entries, part 13.
60. gbest14.seq - EST (expressed sequence tag) sequence entries, part 14.
61. gbest15.seq - EST (expressed sequence tag) sequence entries, part 15.
62. gbest16.seq - EST (expressed sequence tag) sequence entries, part 16.
63. gbest17.seq - EST (expressed sequence tag) sequence entries, part 17.
64. gbest18.seq - EST (expressed sequence tag) sequence entries, part 18.
65. gbest19.seq - EST (expressed sequence tag) sequence entries, part 19.
66. gbest20.seq - EST (expressed sequence tag) sequence entries, part 20.
67. gbest21.seq - EST (expressed sequence tag) sequence entries, part 21.
68. gbest22.seq - EST (expressed sequence tag) sequence entries, part 22.
69. gbest23.seq - EST (expressed sequence tag) sequence entries, part 23.
70. gbest24.seq - EST (expressed sequence tag) sequence entries, part 24.
71. gbest25.seq - EST (expressed sequence tag) sequence entries, part 25.
72. gbest26.seq - EST (expressed sequence tag) sequence entries, part 26.
73. gbest27.seq - EST (expressed sequence tag) sequence entries, part 27.
74. gbest28.seq - EST (expressed sequence tag) sequence entries, part 28.
75. gbest29.seq - EST (expressed sequence tag) sequence entries, part 29.
76. gbest30.seq - EST (expressed sequence tag) sequence entries, part 30.
77. gbest31.seq - EST (expressed sequence tag) sequence entries, part 31.
78. gbest32.seq - EST (expressed sequence tag) sequence entries, part 32.
79. gbest33.seq - EST (expressed sequence tag) sequence entries, part 33.
80. gbest34.seq - EST (expressed sequence tag) sequence entries, part 34.
81. gbest35.seq - EST (expressed sequence tag) sequence entries, part 35.
82. gbest36.seq - EST (expressed sequence tag) sequence entries, part 36.
83. gbest37.seq - EST (expressed sequence tag) sequence entries, part 37.
84. gbest38.seq - EST (expressed sequence tag) sequence entries, part 38.
85. gbest39.seq - EST (expressed sequence tag) sequence entries, part 39.
86. gbest40.seq - EST (expressed sequence tag) sequence entries, part 40.
87. gbest41.seq - EST (expressed sequence tag) sequence entries, part 41.
88. gbest42.seq - EST (expressed sequence tag) sequence entries, part 42.
89. gbest43.seq - EST (expressed sequence tag) sequence entries, part 43.
90. gbest44.seq - EST (expressed sequence tag) sequence entries, part 44.
91. gbest45.seq - EST (expressed sequence tag) sequence entries, part 45.
92. gbest46.seq - EST (expressed sequence tag) sequence entries, part 46.
93. gbest47.seq - EST (expressed sequence tag) sequence entries, part 47.
94. gbest48.seq - EST (expressed sequence tag) sequence entries, part 48.
95. gbest49.seq - EST (expressed sequence tag) sequence entries, part 49.
96. gbest50.seq - EST (expressed sequence tag) sequence entries, part 50.
97. gbest51.seq - EST (expressed sequence tag) sequence entries, part 51.
98. gbest52.seq - EST (expressed sequence tag) sequence entries, part 52.
99. gbest53.seq - EST (expressed sequence tag) sequence entries, part 53.
100. gbest54.seq - EST (expressed sequence tag) sequence entries, part 54.
101. gbest55.seq - EST (expressed sequence tag) sequence entries, part 55.
102. gbest56.seq - EST (expressed sequence tag) sequence entries, part 56.
103. gbest57.seq - EST (expressed sequence tag) sequence entries, part 57.
104. gbest58.seq - EST (expressed sequence tag) sequence entries, part 58.
105. gbest59.seq - EST (expressed sequence tag) sequence entries, part 59.
106. gbest60.seq - EST (expressed sequence tag) sequence entries, part 60.
107. gbest61.seq - EST (expressed sequence tag) sequence entries, part 61.
108. gbest62.seq - EST (expressed sequence tag) sequence entries, part 62.
109. gbest63.seq - EST (expressed sequence tag) sequence entries, part 63.
110. gbest64.seq - EST (expressed sequence tag) sequence entries, part 64.
111. gbest65.seq - EST (expressed sequence tag) sequence entries, part 65.
112. gbest66.seq - EST (expressed sequence tag) sequence entries, part 66.
113. gbest67.seq - EST (expressed sequence tag) sequence entries, part 67.
114. gbest68.seq - EST (expressed sequence tag) sequence entries, part 68.
115. gbest69.seq - EST (expressed sequence tag) sequence entries, part 69.
116. gbest70.seq - EST (expressed sequence tag) sequence entries, part 70.
117. gbest71.seq - EST (expressed sequence tag) sequence entries, part 71.
118. gbest72.seq - EST (expressed sequence tag) sequence entries, part 72.
119. gbest73.seq - EST (expressed sequence tag) sequence entries, part 73.
120. gbest74.seq - EST (expressed sequence tag) sequence entries, part 74.
121. gbest75.seq - EST (expressed sequence tag) sequence entries, part 75.
122. gbest76.seq - EST (expressed sequence tag) sequence entries, part 76.
123. gbest77.seq - EST (expressed sequence tag) sequence entries, part 77.
124. gbest78.seq - EST (expressed sequence tag) sequence entries, part 78.
125. gbest79.seq - EST (expressed sequence tag) sequence entries, part 79.
126. gbest80.seq - EST (expressed sequence tag) sequence entries, part 80.
127. gbest81.seq - EST (expressed sequence tag) sequence entries, part 81.
128. gbest82.seq - EST (expressed sequence tag) sequence entries, part 82.
129. gbest83.seq - EST (expressed sequence tag) sequence entries, part 83.
130. gbest84.seq - EST (expressed sequence tag) sequence entries, part 84.
131. gbest85.seq - EST (expressed sequence tag) sequence entries, part 85.
132. gbest86.seq - EST (expressed sequence tag) sequence entries, part 86.
133. gbest87.seq - EST (expressed sequence tag) sequence entries, part 87.
134. gbest88.seq - EST (expressed sequence tag) sequence entries, part 88.
135. gbest89.seq - EST (expressed sequence tag) sequence entries, part 89
136. gbest90.seq - EST (expressed sequence tag) sequence entries, part 90.
137. gbest91.seq - EST (expressed sequence tag) sequence entries, part 91.
138. gbest92.seq - EST (expressed sequence tag) sequence entries, part 92.
139. gbest93.seq - EST (expressed sequence tag) sequence entries, part 93.
140. gbest94.seq - EST (expressed sequence tag) sequence entries, part 94.
141. gbest95.seq - EST (expressed sequence tag) sequence entries, part 95.
142. gbest96.seq - EST (expressed sequence tag) sequence entries, part 96.
143. gbest97.seq - EST (expressed sequence tag) sequence entries, part 97.
144. gbest98.seq - EST (expressed sequence tag) sequence entries, part 98.
145. gbest99.seq - EST (expressed sequence tag) sequence entries, part 99.
146. gbest100.seq - EST (expressed sequence tag) sequence entries, part 100.
147. gbest101.seq - EST (expressed sequence tag) sequence entries, part 101.
148. gbest102.seq - EST (expressed sequence tag) sequence entries, part 102.
149. gbest103.seq - EST (expressed sequence tag) sequence entries, part 103.
150. gbest104.seq - EST (expressed sequence tag) sequence entries, part 104.
151. gbest105.seq - EST (expressed sequence tag) sequence entries, part 105.
152. gbest106.seq - EST (expressed sequence tag) sequence entries, part 106.
153. gbest107.seq - EST (expressed sequence tag) sequence entries, part 107.
154. gbest108.seq - EST (expressed sequence tag) sequence entries, part 108.
155. gbest109.seq - EST (expressed sequence tag) sequence entries, part 109.
156. gbest110.seq - EST (expressed sequence tag) sequence entries, part 110.
157. gbest111.seq - EST (expressed sequence tag) sequence entries, part 111.
158. gbpat1.seq  - Patent sequence entries, part 1.
159. gbpat2.seq  - Patent sequence entries, part 2.
160. gbsts1.seq  - STS (sequence tagged site) sequence entries, part 1.
161. gbsts2.seq  - STS (sequence tagged site) sequence entries, part 2.
162. gbsts3.seq  - STS (sequence tagged site) sequence entries, part 3.
163. gbgss1.seq  - GSS (genome survey sequence) sequence entries, part 1.
164. gbgss2.seq  - GSS (genome survey sequence) sequence entries, part 2.
165. gbgss3.seq  - GSS (genome survey sequence) sequence entries, part 3.
166. gbgss4.seq  - GSS (genome survey sequence) sequence entries, part 4.
167. gbgss5.seq  - GSS (genome survey sequence) sequence entries, part 5.
168. gbgss6.seq  - GSS (genome survey sequence) sequence entries, part 6.
169. gbgss7.seq  - GSS (genome survey sequence) sequence entries, part 7.
170. gbgss8.seq  - GSS (genome survey sequence) sequence entries, part 8.
171. gbgss9.seq  - GSS (genome survey sequence) sequence entries, part 9.
172. gbgss10.seq - GSS (genome survey sequence) sequence entries, part 10.
173. gbgss11.seq - GSS (genome survey sequence) sequence entries, part 11.
174. gbgss12.seq - GSS (genome survey sequence) sequence entries, part 12.
175. gbgss13.seq - GSS (genome survey sequence) sequence entries, part 13.
176. gbgss14.seq - GSS (genome survey sequence) sequence entries, part 14.
177. gbgss15.seq - GSS (genome survey sequence) sequence entries, part 15.
178. gbgss16.seq - GSS (genome survey sequence) sequence entries, part 16.
179. gbgss17.seq - GSS (genome survey sequence) sequence entries, part 17.
180. gbgss18.seq - GSS (genome survey sequence) sequence entries, part 18.
181. gbgss19.seq - GSS (genome survey sequence) sequence entries, part 19.
182. gbgss20.seq - GSS (genome survey sequence) sequence entries, part 20.
183. gbgss21.seq - GSS (genome survey sequence) sequence entries, part 21.
184. gbgss22.seq - GSS (genome survey sequence) sequence entries, part 22.
185. gbgss23.seq - GSS (genome survey sequence) sequence entries, part 23.
186. gbgss24.seq - GSS (genome survey sequence) sequence entries, part 24.
187. gbgss25.seq - GSS (genome survey sequence) sequence entries, part 25.
188. gbgss26.seq - GSS (genome survey sequence) sequence entries, part 26.
189. gbgss27.seq - GSS (genome survey sequence) sequence entries, part 27.
190. gbgss28.seq - GSS (genome survey sequence) sequence entries, part 28.
191. gbgss29.seq - GSS (genome survey sequence) sequence entries, part 29.
192. gbgss30.seq - GSS (genome survey sequence) sequence entries, part 30.
193. gbgss31.seq - GSS (genome survey sequence) sequence entries, part 31.
194. gbgss32.seq - GSS (genome survey sequence) sequence entries, part 32.
195. gbgss33.seq - GSS (genome survey sequence) sequence entries, part 33.
196. gbgss34.seq - GSS (genome survey sequence) sequence entries, part 34.
197. gbgss35.seq - GSS (genome survey sequence) sequence entries, part 35.
198. gbgss36.seq - GSS (genome survey sequence) sequence entries, part 36.
199. gbgss37.seq - GSS (genome survey sequence) sequence entries, part 37.
200. gbhtg1.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 1.
201. gbhtg2.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 2.
202. gbhtg3.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 3.
203. gbhtg4.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 4.
204. gbhtg5.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 5.
205. gbhtg6.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 6.
206. gbhtg7.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 7.
207. gbhtg8.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 8.
208. gbhtg9.seq  - HTGS (high throughput genomic sequencing) sequence entries, part 9.
209. gbhtg10.seq - HTGS (high throughput genomic sequencing) sequence entries, part 10.
210. gbhtg11.seq - HTGS (high throughput genomic sequencing) sequence entries, part 11.
211. gbhtg12.seq - HTGS (high throughput genomic sequencing) sequence entries, part 12.
212. gbhtg13.seq - HTGS (high throughput genomic sequencing) sequence entries, part 13.
213. gbhtg14.seq - HTGS (high throughput genomic sequencing) sequence entries, part 14.
214. gbhtg15.seq - HTGS (high throughput genomic sequencing) sequence entries, part 15.
215. gbhtg16.seq - HTGS (high throughput genomic sequencing) sequence entries, part 16.
216. gbhtg17.seq - HTGS (high throughput genomic sequencing) sequence entries, part 17.
217. gbhtg18.seq - HTGS (high throughput genomic sequencing) sequence entries, part 18.
218. gbhtg19.seq - HTGS (high throughput genomic sequencing) sequence entries, part 19.
219. gbhtg20.seq - HTGS (high throughput genomic sequencing) sequence entries, part 20.
220. gbhtg21.seq - HTGS (high throughput genomic sequencing) sequence entries, part 21.
221. gbhtg22.seq - HTGS (high throughput genomic sequencing) sequence entries, part 22.
222. gbhtg23.seq - HTGS (high throughput genomic sequencing) sequence entries, part 23.
223. gbhtg24.seq - HTGS (high throughput genomic sequencing) sequence entries, part 24.
224. gbhtg25.seq - HTGS (high throughput genomic sequencing) sequence entries, part 25.
225. 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://ncbi.nlm.nih.gov/genbank/README.genbank

2.2.5 File Sizes

  Uncompressed, the Release 123.0 flatfiles require roughly XXXXX MB
(sequence files only) or XXXXX MB (including the 'index' files).  The
following table contains the approximate sizes of the individual files
in this release.  Since minor changes to some of the files may occur
after these release notes have been written, these sizes should not be
used to determine file integrity; they are provided as an aid to planning
only.

File Size      File Name

373731682      gbacc.idx
500577963      gbaut1.idx
501772521      gbaut2.idx
502534275      gbaut3.idx
500025159      gbaut4.idx
502873959      gbaut5.idx
511393948      gbaut6.idx
501282921      gbaut7.idx
501866010      gbaut8.idx
 53346914      gbaut9.idx
250000187      gbbct1.seq
250000443      gbbct2.seq
220915166      gbbct3.seq
  2943818      gbchg.txt
   453294      gbdel.txt
229697084      gbest1.seq
230687671      gbest10.seq
230689175      gbest100.seq
230689789      gbest101.seq
230688277      gbest102.seq
230688942      gbest103.seq
230687982      gbest104.seq
230690239      gbest105.seq
230688256      gbest106.seq
230689353      gbest107.seq
227238010      gbest108.seq
227495255      gbest109.seq
230689828      gbest11.seq
230690448      gbest110.seq
 88946211      gbest111.seq
230688484      gbest12.seq
230689185      gbest13.seq
230690416      gbest14.seq
230688574      gbest15.seq
230688025      gbest16.seq
230689099      gbest17.seq
230687725      gbest18.seq
230689289      gbest19.seq
226685633      gbest2.seq
230688212      gbest20.seq
230690459      gbest21.seq
230689357      gbest22.seq
230690344      gbest23.seq
230687842      gbest24.seq
230688094      gbest25.seq
230688659      gbest26.seq
230689116      gbest27.seq
230690414      gbest28.seq
230687946      gbest29.seq
227447182      gbest3.seq
230687925      gbest30.seq
219567523      gbest31.seq
187520126      gbest32.seq
186994507      gbest33.seq
213544115      gbest34.seq
212491099      gbest35.seq
212688638      gbest36.seq
213878811      gbest37.seq
230688793      gbest38.seq
230687856      gbest39.seq
230690468      gbest4.seq
215933842      gbest40.seq
230688236      gbest41.seq
230688542      gbest42.seq
230688735      gbest43.seq
230689672      gbest44.seq
230689083      gbest45.seq
230687669      gbest46.seq
230690148      gbest47.seq
230688733      gbest48.seq
230690669      gbest49.seq
162074881      gbest5.seq
230690397      gbest50.seq
230689105      gbest51.seq
227729515      gbest52.seq
230688496      gbest53.seq
214932923      gbest54.seq
205721427      gbest55.seq
205377558      gbest56.seq
204962673      gbest57.seq
204657390      gbest58.seq
204849516      gbest59.seq
174892757      gbest6.seq
204619712      gbest60.seq
204588259      gbest61.seq
205837308      gbest62.seq
205101073      gbest63.seq
201360568      gbest64.seq
202232677      gbest65.seq
202732750      gbest66.seq
203007494      gbest67.seq
216352557      gbest68.seq
230687570      gbest69.seq
230689014      gbest7.seq
230689689      gbest70.seq
230687495      gbest71.seq
230689287      gbest72.seq
230689254      gbest73.seq
230687797      gbest74.seq
230690201      gbest75.seq
230688705      gbest76.seq
230689346      gbest77.seq
230688991      gbest78.seq
230687940      gbest79.seq
230688821      gbest8.seq
230688367      gbest80.seq
230689928      gbest81.seq
230689870      gbest82.seq
230687546      gbest83.seq
230687733      gbest84.seq
230690543      gbest85.seq
230690155      gbest86.seq
230688291      gbest87.seq
230689704      gbest88.seq
230688286      gbest89.seq
230689074      gbest9.seq
230687742      gbest90.seq
230690429      gbest91.seq
230687620      gbest92.seq
229419437      gbest93.seq
228750929      gbest94.seq
230688052      gbest95.seq
230689966      gbest96.seq
230688824      gbest97.seq
230688681      gbest98.seq
230690088      gbest99.seq
 14998890      gbgen.idx
 14882478      gbgss1.seq
209716722      gbgss10.seq
209716918      gbgss11.seq
209717400      gbgss12.seq
209718289      gbgss13.seq
209716519      gbgss14.seq
209719149      gbgss15.seq
209716311      gbgss16.seq
209716388      gbgss17.seq
209716398      gbgss18.seq
209414543      gbgss19.seq
250001837      gbgss2.seq
209718132      gbgss20.seq
209717038      gbgss21.seq
209719166      gbgss22.seq
209716935      gbgss23.seq
209718639      gbgss24.seq
209717574      gbgss25.seq
209716843      gbgss26.seq
209719090      gbgss27.seq
209716112      gbgss28.seq
209717991      gbgss29.seq
250002019      gbgss3.seq
209717441      gbgss30.seq
209718434      gbgss31.seq
209716092      gbgss32.seq
209718226      gbgss33.seq
209717522      gbgss34.seq
209716494      gbgss35.seq
 53611691      gbgss36.seq
132974298      gbgss37.seq
250003139      gbgss4.seq
250001097      gbgss5.seq
179130777      gbgss6.seq
209717746      gbgss7.seq
209717443      gbgss8.seq
209716347      gbgss9.seq
135887064      gbhtc.seq
250158266      gbhtg1.seq
250137081      gbhtg10.seq
250166278      gbhtg11.seq
250001220      gbhtg12.seq
250167603      gbhtg13.seq
250120097      gbhtg14.seq
250142493      gbhtg15.seq
250172204      gbhtg16.seq
250147622      gbhtg17.seq
250036667      gbhtg18.seq
250017312      gbhtg19.seq
250111169      gbhtg2.seq
250083194      gbhtg20.seq
250003826      gbhtg21.seq
250025046      gbhtg22.seq
250026085      gbhtg23.seq
250176135      gbhtg24.seq
126723014      gbhtg25.seq
250085539      gbhtg3.seq
250186606      gbhtg4.seq
250018436      gbhtg5.seq
250183594      gbhtg6.seq
250127910      gbhtg7.seq
250135406      gbhtg8.seq
250194006      gbhtg9.seq
250075488      gbinv1.seq
250002382      gbinv2.seq
250009395      gbinv3.seq
 42942451      gbinv4.seq
333936143      gbjou.idx
265859805      gbkey.idx
 90683427      gbmam.seq
 10268199      gbnew.txt
250001934      gbpat1.seq
164940791      gbpat2.seq
 13404677      gbphg.seq
250001927      gbpln1.seq
250122007      gbpln2.seq
250021720      gbpln3.seq
114408699      gbpln4.seq
250103770      gbpri1.seq
176171096      gbpri10.seq
250130514      gbpri2.seq
250030706      gbpri3.seq
250000477      gbpri4.seq
250000196      gbpri5.seq
250031565      gbpri6.seq
250086676      gbpri7.seq
250002385      gbpri8.seq
250001431      gbpri9.seq
   111216      gbrel.txt
250013740      gbrod1.seq
 50558753      gbrod2.seq
923659554      gbsdr.txt
  1101122      gbsec.idx
250002675      gbsts1.seq
250002256      gbsts2.seq
   300540      gbsts3.seq
 24139082      gbsyn.seq
  1399038      gbuna.seq
250000650      gbvrl1.seq
144385053      gbvrl2.seq
168777519      gbvrt.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         28721      99571484
BCT2         40276      101607804
BCT3         35943      81453717
EST1         68601      26480147
EST10        77322      30120249
EST100       75718      51468463
EST101       70287      45580178
EST102       76776      44404462
EST103       117849     42705819
EST104       88537      28973512
EST105       71050      25168832
EST106       75061      28032147
EST107       74400      26484974
EST108       79254      26929432
EST109       73188      26960656
EST11        76242      29024580
EST110       69197      29570214
EST111       33121      11100988
EST12        77933      31017495
EST13        77656      29461934
EST14        80186      32453800
EST15        73367      31034491
EST16        75875      33262910
EST17        84239      34456995
EST18        80661      32557431
EST19        81351      33741085
EST2         74335      28516116
EST20        72802      29190643
EST21        73149      33969326
EST22        77414      30820300
EST23        77249      32040677
EST24        75999      34574313
EST25        73321      31085181
EST26        76135      31272736
EST27        79978      35793421
EST28        76664      41071784
EST29        82432      59295116
EST3         73507      29815639
EST30        104393     48047904
EST31        85711      38541178
EST32        68853      18099440
EST33        68849      17849223
EST34        61945      18211064
EST35        43651      10689524
EST36        43217      10959606
EST37        43065      10524315
EST38        82191      33380601
EST39        99549      45210893
EST4         74843      28464386
EST40        92333      48524121
EST41        80458      37701471
EST42        73517      30865450
EST43        72864      32410063
EST44        71548      31082544
EST45        74685      31241839
EST46        83217      32758353
EST47        70226      27598273
EST48        66480      30912285
EST49        73283      31569761
EST5         48091      15267864
EST50        81519      36889940
EST51        72730      30581220
EST52        73933      26293131
EST53        88086      39746975
EST54        52463      17814288
EST55        40062      10137967
EST56        40066      11044524
EST57        40353      11568927
EST58        40529      10866682
EST59        40457      11276149
EST6         54654      17337071
EST60        40468      11511106
EST61        40359      11198844
EST62        40059      11128666
EST63        40477      11257041
EST64        41396      11004359
EST65        41075      11331294
EST66        41001      11540109
EST67        41025      11497422
EST68        45225      11213696
EST69        72149      31077316
EST7         75053      29550911
EST70        74876      28738869
EST71        76511      31737332
EST72        79276      44930110
EST73        79026      41617644
EST74        77519      41957858
EST75        79673      37841761
EST76        71816      42014051
EST77        75915      36721848
EST78        76598      38654692
EST79        70894      37185387
EST8         76571      30815907
EST80        78384      51176461
EST81        68572      35313205
EST82        73634      37146227
EST83        73727      41554918
EST84        74483      44643021
EST85        76462      48233552
EST86        75140      38153557
EST87        70838      31394412
EST88        67235      32122098
EST89        68115      41513117
EST9         78378      30196749
EST90        78162      41617370
EST91        71218      42926520
EST92        76970      34462878
EST93        73809      30482821
EST94        75532      28189899
EST95        73897      41172314
EST96        68989      36094821
EST97        79155      46617362
EST98        75760      48896667
EST99        72196      43473734
GSS1         6511       3531425
GSS10        72154      38576312
GSS11        71343      35739949
GSS12        71899      36090847
GSS13        72180      36924095
GSS14        69283      34442083
GSS15        67712      35234174
GSS16        70271      40709342
GSS17        62186      32072032
GSS18        68810      35908425
GSS19        68213      34990965
GSS2         86967      65925009
GSS20        66168      29806431
GSS21        63936      31633796
GSS22        73404      43853565
GSS23        65795      30836913
GSS24        58386      26946536
GSS25        52380      27390808
GSS26        53093      25536006
GSS27        54087      22980424
GSS28        59497      37409227
GSS29        55760      24277281
GSS3         75231      63116406
GSS30        54581      32265301
GSS31        67920      36956168
GSS32        56822      21577343
GSS33        53378      24778857
GSS34        66919      30569703
GSS35        85360      40713200
GSS36        21349      8954387
GSS37        51502      22545611
GSS4         74525      63451323
GSS5         88221      64537246
GSS6         71379      30100334
GSS7         85698      35916851
GSS8         81527      38713265
GSS9         75725      38719621
HTC          19168      23439085
HTG1         1312       191767486
HTG10        1201       189455250
HTG11        1233       189304708
HTG12        17932      162245260
HTG13        22021      156675452
HTG14        1253       188571000
HTG15        4505       184964616
HTG16        5422       184090763
HTG17        4731       183826523
HTG18        5687       179686213
HTG19        1670       186449027
HTG2         1272       189955619
HTG20        1147       192928083
HTG21        1146       192513871
HTG22        1131       193054528
HTG23        1170       190360821
HTG24        1158       192588761
HTG25        591        94042482
HTG3         1221       190350148
HTG4         3129       188508259
HTG5         1639       189188804
HTG6         2715       190644566
HTG7         1225       189848149
HTG8         1242       189422877
HTG9         1292       188609307
INV1         6813       171423270
INV2         46560      113843176
INV3         22028      131285757
INV4         12209      14801667
MAM          30048      26447003
PAT1         193052     77547451
PAT2         117554     46241514
PHG          1699       5071048
PLN1         34293      125446791
PLN2         41369      114179762
PLN3         60315      92699415
PLN4         17947      49111815
PRI1         8436       164736119
PRI10        42947      69324414
PRI2         1372       175890535
PRI3         1313       184802229
PRI4         12699      166851270
PRI5         27959      136235307
PRI6         1551       174977852
PRI7         13612      163717391
PRI8         19967      146362395
PRI9         32701      129233483
ROD1         52132      106596831
ROD2         13633      17623817
STS1         67652      54184246
STS2         89781      34635836
STS3         159        75497
SYN          4404       11072720
UNA          668        337508
VRL1         74936      64237088
VRL2         43729      39445338
VRT          54414      49438550

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 123.0 (chloroplast and mitochon-
drial sequences not included):

Entries      Bases   Species

4544962 7387490518   Homo sapiens
2793543 1527228639   Mus musculus
167687   502655942   Drosophila melanogaster
183987   249689164   Arabidopsis thaliana
114744   204396881   Caenorhabditis elegans
161411   171870798   Oryza sativa
189000   165542107   Tetraodon nigroviridis
229838   114331466   Rattus norvegicus
168469    76700774   Bos taurus
167090    73450470   Glycine max
120670    60606228   Medicago truncatula
109913    56462749   Lycopersicon esculentum
91360     50723464   Trypanosoma brucei
70317     49770458   Hordeum vulgare
56451     49431105   Giardia intestinalis
77554     47633412   Strongylocentrotus purpuratus
93141     47584911   Danio rerio
92041     46517145   Xenopus laevis
98818     45978459   Zea mays
49969     44552032   Entamoeba histolytica

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.
Over the period 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

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 225 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 2001

                NCBI-GenBank Flat File Release 123.0

                        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. Beneath each index key, the identifiers of the
sequence entries containing that index key are listed (LOCUS name,
division abbreviation, and primary accession number). The following
codes are used to designate the data file divisions:

 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
term is presented on its own line, and is followed by a
LOCUS/Division/Accession triplet for every record containing the term:

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 terms 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 term (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 four subkeywords and may repeat. Mandatory
keyword/one or more records.

   AUTHORS	- Lists the authors of the citation. Mandatory
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 pieces of information contained in the LOCUS record are always
found in fixed positions. The locus name (or entry name), which is
always ten 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 29.
The letters `bp' are in positions 31 to 32. Positions 34 to 36 give
the number of strands of the sequence. Positions 37 to 40 give the
topology of molecule sequenced. If the sequence is of a special type,
a notation (such as `circular') is included in positions 43 to 52.

  GenBank sequence entries are divided among sixteen different
divisions. Each entry's division is specified by a three-letter code
in positions 53 to 55. See Section 3.3 for an explanation of division
codes.

  Positions 63 to 73 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 record is as follows:

Positions   	Contents

1-12	LOCUS
13-22	Locus name
23-29	Length of sequence, right-justified
31-32	bp
34-36	Blank, ss- (single-stranded), ds- (double-stranded), or
	 ms- (mixed-stranded)
37-41	Blank, DNA, RNA, tRNA (transfer RNA), rRNA (ribosomal RNA), 
	mRNA (messenger RNA), uRNA (small nuclear RNA), snRNA, or scRNA
43-52	Blank (implies linear) or circular
53-55	The division code (see Section 3.3)
63-73	Date, in the form dd-MMM-yyyy (e.g., 15-MAR-1991)

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;

8. A literal sequence (a string of bases enclosed in quotation marks).

  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.

group (location, location, .. location): The elements are related and
should be grouped together, but no order is implied.

one-of (location, location, .. location): The element can be any one,
but only one, of the items listed.

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 'ncbi.nlm.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 only via
anonymous ftp from :

	ftp://ncbi.nlm.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).

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://ncbi.nlm.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 to 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 123.0) 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
	John Anderson, Maureen Beanan, Matthew Beyers, Medha Bhagwat,
	Lori Black, Larry Chlumsky, Karen Clark, Irene Fang, Michael
	Fetchko, Jeff Gilmour, Irene Kim, Pierre Ledoux, Richard
	McVeigh, Leonie Misquitta, Michael Murphy, Cynthia
	Rothblum-Oviatt, Quy Phung, Leigh Riley, Susan Schafer, Suh-suh
	Wang, Jane Weisemann, Steven Wilhite, Sandhya Xirasagar,
	Roxanne Yamashita and Linda Yankie

Data Management and Preparation
	Vladimir Alekseyev, Serge Bazhin, Anton Butanaev, Mark Cavanaugh,
	Hsiu-Chuan Chen, Jim Ostell, Joel Plotkin, Sergei Shavirin,
	Karl Sirotkin, Vladimir Soussov, Tatiana Tatusov, Carolyn Tolstoshev,
	Jane Weisemann

Database Administration
	Slava Khotomliansky, Eugene Yaschenko

Production and User Support
        Dennis Benson, Peter Cooper, Jim Fleshman, Susan Kimball, 
	Renata McCarthy, Scott McGinnis, Monica Romiti, Barbara Rapp, 
	Steven Rosenthal, 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:

  GenBank
  National Library of Medicine
  Bldg. 38A Rm. 8N-809
  8600 Rockville Pike
  Bethesda, MD 20894
  FAX: (301) 480-9241
Support Center