Release Notes For GenBank Release 82

GBREL.TXT          Genetic Sequence Data Bank
                         15 April 1994

                  GenBank Flat File Release 82.0

                Distribution CD-ROM Release Notes

  169896 loci, 180589455 bases, from 169896 reported sequences

  This document describes the data written on GenBank flat file
distribution CD-ROMs. If you have any questions or comments about the
data bank, the CD-ROM, 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


1. INTRODUCTION

1.1 Release 82.0

  On September 30, 1992, the National Center for Biotechnology Information
(NCBI) at the National Library of Medicine (NLM) assumed responsibility for
the GenBank Sequence Data Bank.  NCBI handles all GenBank direct submission
data and authors are advised to use the address below.  Submitters are
encouraged to use the free Authorin software package for sending sequence
data.  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

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

  Release 82.0 is a release of sequence data by NCBI in the GenBank flat file
format.  It contains a large number of entries produced at the NLM, derived
from scanning the biomedical literature. 

  At the NLM, sequence entries are created by specialized indexers in the
Division of Library Operations.  Over 325,000 articles per year from 3400
journals are scanned for sequence data. They are supplemented by journals
in plant and veterinary sciences through a collaboration with the National
Agricultural Library.  These records join the direct submission data stream
and submissions from the European Molecular Biology Laboratory (EMBL) Data
Library and the DNA Database of Japan (DDBJ) for incorporation within a
relational database, GenBank.  The database is converted to various
output formats including the Flat File and Abstract Syntax Notation 1
(ASN.1) versions.  The ASN.1 form of the data is included on the
Entrez: Sequences CD-ROM and is also available, as is the flat file, by
anonymous FTP to 'ncbi.nlm.nih.gov'.

1.2 Cutoff Date

  This full release, 82.0, incorporates data available to the databases as
of March 30, 1994.  For more recent data, users are advised to download
the update files by anonymous FTP to 'ncbi.nlm.nih.gov' or to search the
updates via the e-mail server.  For instructions, send a mail message with the
word 'help' in it to:  retrieve@ncbi.nlm.nih.gov

1.3 Important Changes in Release 82.0

   No changes have been implemented for Release 82.0

1.4 Upcoming Changes

   As announced in the Release 81.0 GenBank release notes, we are planning to
introduce a new division, GBSTS.SEQ, originally scheduled for inclusion in
Release 82.0. However, due to difficulities in reliably identifying all the STS
sequences that are currently scattered across the 14 divisions, we have opted
to temporarily delay the introduction of this new division.

   The STS division is intended to facilitate cross comparison of STSs with
sequences in other divisions for the purpose of correlating map positions of
anonymous sequences with known genes. Because STS data is usually submitted in
bulk form, i.e. many sequences at once, new and easier submission procedures are
being developed and we encourage laboratories producing this type of data to
contact us for more details.

1.5 Request for Direct Submission of Sequence Data

  A successful GenBank requires that the data enter the data bank 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 complete, accurate, and timely data. To
assist researchers in entering their own sequence data, GenBank has
developed AUTHORIN, an easy-to-use program that enables authors to
enter a sequence, annotate it, and submit it to GenBank or any of the
other data banks.  NCBI distributes versions of authorin for IBM
PC-compatibles and the Macintosh. Contact NCBI by phone at 301-496-2475
or by electronic mail:  authorin@ncbi.nlm.nih.gov

  For those who are unable to use the AUTHORIN program, GenBank has a
printed data submission form. This form is now standardized among
EMBL, DDBJ, GenBank, PIR, MIPS, and JIPID. GenBank also provides a
corresponding computer-readable data submission form that can be used
for electronic mail and floppy disk submissions. The GenBank Data
Submission Form (located in the file GBDAT.FRM) can be used to submit
your sequence and annotations. Electronic mail submissions should go
to: gb-sub@ncbi.nlm.nih.gov.  Direct mail should go to:

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

1.6 Organization of This Document

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


2. ORGANIZATION OF CD-ROM FILES

2.1 CD-ROM Format

  The GenBank CD-ROM distribution files are available on ISO-9660
compatible CD-ROM. The data are written as ASCII files with variable
length records. Each record corresponds to one line in the data bank;
a carriage return/line feed pair terminate each line.

The data on the CD-ROMs have both uppercase and lowercase characters.

2.2 Files

  The GenBank flat file release consists of twenty-two files on the
CD-ROM. 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. gbaut.idx 	- Index of the entries according to author.
 6. gbjou.idx 	- Index of the entries according to journal citation.
 7. gbgen.idx 	- Index of the entries according to gene names.
 8. gbdat.frm 	- Forms for submitting sequences or corrections to GenBank.
 9. gbpri.seq 	- Primate sequence entries.
10. gbrod.seq 	- Rodent sequence entries.
11. gbmam.seq 	- Other mammalian sequence entries.
12. gbvrt.seq 	- Other vertebrate sequence entries.
13. gbinv.seq 	- Invertebrate sequence entries.
14. gbpln.seq 	- Plant sequence entries (including fungi and algae).
15. gbbct.seq 	- Bacterial sequence entries.
16. gbrna.seq 	- Structural RNA sequence entries.
17. gbvrl.seq 	- Viral sequence entries.
18. gbphg.seq 	- Phage sequence entries.
19. gbsyn.seq 	- Synthetic and chimeric sequence entries.
20. gbuna.seq 	- Unannotated sequence entries.
21. gbest.seq 	- EST (expressed sequence tag) sequence entries.
22. gbpat.seq 	- patent sequence entries.

2.2.5 File Sizes

  The following table indicates the approximate sizes of the individual files
in this release.  Since minor changes to some of the files may occur after the
release notes are written, these sizes should not be used to determine file
integrity.  They are provided as an aid to planning only.

File Size      File Name

 6646597       gbacc.idx
23575620       gbaut.idx
70332429       gbbct.seq
66916445       gbest.seq
 1732422       gbgen.idx
   23593       gbdat.frm
47143614       gbinv.seq
10340336       gbjou.idx
 9303373       gbkey.idx
18445799       gbmam.seq
 6600288       gbpat.seq
 3992176       gbphg.seq
68480735       gbpln.seq
98018000       gbpri.seq
   77158       gbrel.txt
 7438045       gbrna.seq
67713881       gbrod.seq
13762501       gbsdr.txt
 6299484       gbsyn.seq
 3133594       gbuna.seq
59004927       gbvrl.seq
21269741       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 in each sequence
data file:

Division     Entries         Bases

BCT            15107      27433286
EST            33727      10672722
INV            11234      18729402
MAM             5628       6183786
PAT             5281       1831626
PHG              968       1414274
PLN            16154      27150929
PRI            31972      30328835
RNA             3603       2176197
ROD            20581      22836624
SYN             1717       2572139
UNA             1490       1391910
VRL            15876      20597295
VRT             6558       7270430

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

Entries      Bases   Species

47668     34016755   Homo sapiens
12955     12236263   Mus musculus
4945       7499511   Rattus norvegicus
2832       6785309   Saccharomyces cerevisiae
2848       5480893   Escherichia coli
5219       5416525   Caenorhabditis elegans
2572       5077250   Drosophila melanogaster
5770       3064428   Arabidopsis thaliana
1901       2518628   Gallus gallus
4716       2159260   Human immunodeficiency virus type 1
5170       2127717   Oryza sativa
1668       2031057   Bos taurus
1155       1581501   Xenopus laevis
1104       1525353   Oryctolagus cuniculus
592        1474294   Bacillus subtilis
1005       1096499   Zea mays
1609       1091225   Plasmodium falciparum
917        1022805   Influenza virus type A
64          809013   Mycobacterium leprae
403         797986   Schizosaccharomyces pombe

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 21 months.


Release   Date      Base Pairs   Entries

    3    Dec 82         680338       606
   14    Nov 83        2274029      2427
   20    May 84        3002088      3665
   24    Sep 84        3323270      4135
   25    Oct 84        3368765      4175
   26    Nov 84        3689752      4393
   32    May 85        4211931      4954
   36    Sep 85        5204420      5700
   40    Feb 86        5925429      6642
   42    May 86        6765476      7416
   44    Aug 86        8442357      8823
   46    Nov 86        9615371      9978
   48    Feb 87       10961380     10913
   50    May 87       13048473     12534
   52    Aug 87       14855145     14020
   53    Sep 87       15514776     14584
   54    Dec 87       16752872     15465
   55    Mar 88       19156002     17047
   56    Jun 88       20795279     18226
   57    Sep 88       22019698     19044
   57.1  Oct 88       23800000     20579
   58    Dec 88       24690876     21248
   59    Mar 89       26382491     22479
   60    Jun 89       31808784     26317
   61    Sep 89       34762585     28791
   62    Dec 89       37183950     31229
   63    Mar 90       40127752     33377
   64    Jun 90       42495893     35100
   65    Sep 90       49179285     39533
   66    Dec 90       51306092     41057
   67    Mar 91       55169276     43903
   68    Jun 91       65868799     51418
   69    Sep 91       71947426     55627
   70    Dec 91       77337678     58952
   71    Mar 92       83894652     65100
   72    Jun 92       92160761     71280
   73    Sep 92      101008486     78608
   74    Dec 92      120242234     97084
   75    Feb 93      126212259    106684
   76    Apr 93      129968355    111911
   77    Jun 93      138904393    120134
   78    Aug 93      147215633    131328
   79    Oct 93      157152442    143492
   80    Dec 93      163802597    150744
   81    Feb 94      173261500    162946
   82    Apr 94      180589455    169896



3. FILE FORMATS

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

3.1 File Header Information

  Each of the twenty-one files on the distribution CD-ROM 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 data bank name (Genetic Sequence Data Bank) starting in
column 20. 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 26. The fourth line contains
the current GenBank release number. The release number appears in
positions 41 to 45 and consists of two 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 7, the number of bases in positions 15 to 23, and the
number of reports in positions 37 to 40. (There are more reports of
sequences than entries since reported sequences that overlap or
duplicate each other are combined into single entries.) The third,
fifth, seventh, and ninth lines are blank.

1       10        20        30        40        50        60        70       79
---------+---------+---------+---------+---------+---------+---------+---------
GBACC.IDX          Genetic Sequence Data Bank
                         15 December 1993

                 GenBank Flat File Release 80.0

                      Accession Number Index

  150744 loci, 163802597 bases, from 150744 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
fourteen groups, one group for each of the fourteen 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, or EST. 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 five files containing indices to the entries in this release:

 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. (The index keys
for the keyword phrases and author names appear in uppercase
characters even though they appear in mixed case in the sequence
entries.) Under each index key, the names of the sequence entries
containing that index key are listed alphabetically. Each sequence
name is also followed by its data file division 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. RNA - structural RNA sequences
 9. VRL - viral sequences
10. PHG - bacteriophage sequences
11. SYN - synthetic sequences
12. UNA - unannotated sequences
13. EST - EST sequences
14. PAT - patent sequences

  The index key begins in column 1 of a record. An 11-character field
for the sequence entry name starts in position 14 of a record,
followed by a 3-character field for the data file division, starting
at position 25 and ending at position 27, and a 6-character field for
the primary accession number, starting at position 29 and ending at
position 34. All entries in the fields are left-justified.

  Beginning at positions 36 and 58, the three fields repeat, so three
sets of sequence information can appear in one record. If there are
more than three entry names, the next records are used; the index key
is not repeated. For the accession number files, the entry names begin
in the same record as the index key, since the key is always less than
12 characters. In the other index files, the entry names begin on the
record following the index key record.

3.3.1 Accession Number Index File

  Accession numbers consist of a single letter followed by five digits.
They provide an unchanging designation for the data with which they
are associated, and we encourage you to cite accession numbers
whenever you refer to data from the data bank. The primary accession
number is the first accession number of an entry. It is unique to that
entry. Citation of that number will enable other investigators to
locate the data no matter what entry name changes or other data bank
reorganizations may occur. The accession numbers, however, carry no
intrinsic information about the data.

  In addition to the primary accession number, some entries have
secondary accession numbers. Secondary accession numbers arise for a
number of reasons. For example, a single accession number may
initially be assigned to the sequence in an article. If it is later
discovered that the sequence must be entered into the data bank as
multiple entries, each entry would receive a new primary accession
number; the previous accession number would appear as the secondary
accession number in each entry.

  The following excerpt from the accession number index file illustrates
the format of the index:

1       10        20        30        40        50        60        70       79
---------+---------+---------+---------+---------+---------+---------+---------
J00316       HUMTBB11P  PRI J00316
J00317       HUMTBB46P  PRI J00317
J00318       HUMUG1     PRI J00318
J00319       HUMUG1PA   PRI J00319
J00320       HUMVIPMR1  PRI L00154 HUMVIPMR2  PRI L00155 HUMVIPMR3  PRI L00156
             HUMVIPMR4  PRI L00157 HUMVIPMR5  PRI L00158
J00321       BABA1AT    PRI J00321
J00322       CHPRSA     PRI J00322
J00323       AGMRSASPC  PRI J00323
J00324       BABATIII   PRI J00324
---------+---------+---------+---------+---------+---------+---------+---------
1       10        20        30        40        50        60        70       79

Example 4. Accession Number Index File

  If the same accession number is found in more than one entry (a result
of the infrequent occasions when a single entry is split into two or
more separate entries), then the additional entries and groups in
which the number appears are also given.

3.3.2 Keyword Phrase Index File

  Keyword phrases consist of names for gene products and other
characteristics of sequence entries. There are approximately 18,000
keyword phrases. An excerpt from the keyword phrase index file is
shown below:

1       10        20        30        40        50        60        70       79
---------+---------+---------+---------+---------+---------+---------+---------
DNA HELICASE
             ECOHELIV   BCT J04726 ECOUVRD    BCT X00738 FPLTRAX    BCT M38047
             HS2ULL     VRL D10470 HSECOMGEN  VRL M86664 PT4DDA     PHG M93048
             SYNPMMB190 SYN M37846 YSPRHP3    PLN X64583
DNA HELICASE I
             ECOPTRAI5  BCT X57430
DNA HELICASE II
             ECOUVRD2   BCT D00069 HEAMUTB1A  BCT M99049
DNA INVERSION SYSTEM
             ECOP15BG   BCT X62121
DNA INVERTASE
             ECOPIN     BCT K00676 ECOPIN1    BCT X01805 PMUGINMOM  PHG V01463
             STABINR3   BCT X16298 STAINVSA   BCT M36694
DNA J HEATSHOCK PROTEIN
             MSGDNAJHSP BCT M95576
DNA LIGASE
             ECOLIG     BCT M24278 ECOLIGA    BCT M30255 PT4G30     PHG X00039
             PT6LIG55   PHG M38465 TTHDNALGS  BCT M74792 TTHDNALIG  BCT M36417
             VACCDNLIG  VRL X16512 VACRHF     VRL D11079 YSCCDC9    PLN X03246
             YSPCDC17   PLN X05107 ZMOLIG     BCT Z11910
---------+---------+---------+---------+---------+---------+---------+---------
1       10        20        30        40        50        60        70       79

Example 5. Keyword Phrase Index File


3.3.3 Author Name Index File

The author name index file lists all of the author names that appear
in the citations. An excerpt from the author name index file is shown
below:

1       10        20        30        40        50        60        70       79
---------+---------+---------+---------+---------+---------+---------+---------
JACKSON,D.I.
             RATLCAG1   ROD M18349 RATLCAG2   ROD M18348 RATLCAG3   ROD M18347
             RATLCAI    ROD M25820 RATLCAII   ROD M25821 RATLCAIII  ROD M25822
             RATLCAIV   ROD M25823 RATLCAR    ROD Y00065
JACKSON,F.R.
             DRO16883C  INV X62939 DRO1688ED  INV X62938 DRO1688EP  INV X62937
             DROPER     INV M11969 DROPES     INV X03636 MUSPER     ROD M12039
             MUSURFPER  ROD X02966
JACKSON,I.J.
             MUSHOMA    ROD X03033 MUSNEORP8R ROD X54812 MUSP7H2    ROD X54811
             MUSRPT     ROD M69041 MUSSOFI    ROD X63350 MUSTRP15   ROD X59513
             MUSTYRP2   ROD X63349
JACKSON,I.M.
             RATTRH     ROD M12138
JACKSON,J.
             DROFPS85D  INV X52844 MUSIGKAC3  ROD K00885 MUSIL4RA   ROD M27959
             MUSIL4RB   ROD M27960 RABGLOBCON MAM L05833 RABGLOBHSB MAM L05835
---------+---------+---------+---------+---------+---------+---------+---------
1       10        20        30        40        50        60        70       79

Example 6. Author Name Index File


3.3.4 Journal Citation Index File

  The journal citation index file lists all of the citations that appear
in the references. All citations are truncated to 80 characters. An
excerpt from the citation index file is shown below:

1       10        20        30        40        50        60        70       79
---------+---------+---------+---------+---------+---------+---------+---------
(IN) THE IMMUNE SYSTEM:  132-138, S. KARGER, NEW YORK (1981)
             HUMIGHVX   PRI M35415
(IN) THE LENS: TRANSPARANCY AND CATARACT:  171-179, EURAGE, RIJSWIJK (1986)
             RANCRYG2A  VRT K02264 RANCRYG4A  VRT K02266 RANCRYG5A  VRT M22529
             RANCRYG6A  VRT M22530 RANCRYR    VRT X00659
(IN) THIOREDOXIN AND GLUTAREDOXIN SYSTEMS: STRUCTURE AND FUNCTION: 11-19, UNKNOW
             ECOTRXA1   BCT M54881
(IN) UCLA SYMP. MOL. CELL. BIOL. NEW SER., VOL. 77:  339-352, ALAN R. LISS, INC.
             BOVTRNB2A  MAM M36431 HUMTRNB    PRI M36429 HUMTRNB1   PRI M36430
(IN) UCLA SYMPOSIA:  575-584, ALAN R. LISS, INC., NEW YORK (1987)
             PFAHGPRT   INV M54896
(IN) VIRUS RESEARCH. PROCEEDINGS OF 1973 ICN-UCLA SYMPOSIUM:  533-544, ACADEMIC
             LAMCG      PHG J02459
ACTA BIOCHIM. BIOPHYS. SIN. 23, 246-253 (1992)
             HUMPLASINS PRI M98056
---------+---------+---------+---------+---------+---------+---------+---------
1       10        20        30        40        50        60        70       79

Example 7. Journal Citation Index File


3.3.5 Gene Name Index

  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. An excerpt from the gene name
index file is shown below:

1       10        20        30        40        50        60        70       79
---------+---------+---------+---------+---------+---------+---------+---------
SUPPRESSOR OF SABLE
             DROSUSG    INV M57889
SUPPRESSOR TWO OF ZESTE
             DROS2ZSTG  INV X56798
SUPRESSOR TWO OF ZESTE
             DROS2ZSTM  INV X56799
SUR
             CHKSRVCNTK VRT M57290
SURC
             ARFSURCG   BCT X63435
---------+---------+---------+---------+---------+---------+---------+---------
1       10        20        30        40        50        60        70       79

Example 8. Gene Name Index File


3.4 GenBank Data Submission Form and Error/Suggestion Report Form

  The recommended method for submitting sequence data to GenBank is through
the Authorin program.  Copies for the Macintosh or PC are available free of
charge. For further information, contact NCBI at (301) 496-2475 or at
the following e-mail address:

           authorin@ncbi.nlm.nih.gov

By using Authorin you will be assisting the database in making your
data available as quickly and as efficiently as possible.  

  If it is not possible to use Authorin, there is a data submission
form in this distribution (GBDAT.FRM) which can be filled out with
a text editor and returned to the database, preferably by e-mail.

  Direct submission e-mail address:  gb-sub@ncbi.nlm.nih.gov

  The second form in the GBDAT.FRM is the GenBank Error/Suggestion Report
Form. It is separated from the Data Submission Form by a form-feed
character (<CTRL>L, ASCII octal value 014, ASCII decimal value 12). We
encourage all users to report any errors to the data bank staff
using this form. Like the GenBank Data Submission Form, it may be
printed and filled in by hand and sent by mail to the address given
at the beginning of the form. It may also be filled out using a text
editor and sent to GenBank by electronic mail at:  update@ncbi.nlm.nih.gov


3.5 Sequence Entry Files

  The distribution CD-ROM contains fourteen sequence entry data files, one
for each division of GenBank.

3.5.1 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).

3.5.2  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).

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 5, indicating the nature of an entry
(feature key) in the FEATURES table; these codes are described in
Section 3.5.11.1 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 3.5.4 to 3.5.13.

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.

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.

   STANDARD	- Lists information about the degree to which the
entry has been annotated and the level of review to which it has been
subjected. Mandatory subkeyword/exactly one record.

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.

3.5.3 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
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)
  STANDARD  full automatic
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
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)
  STANDARD  full automatic
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


3.5.4 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 fourteen taxonomic
divisions. Each entry's division is identified by a three-letter code
in positions 53 to 55. See Section 3.3 for the 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)
37-40	Blank, DNA, RNA, tRNA (transfer RNA), rRNA (ribosomal RNA), 
	mRNA (messenger RNA), or uRNA (small nuclear RNA)
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)

3.5.5 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.

3.5.5.1 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.

3.5.6 ACCESSION Format

  This field contains a series of six-character identifiers (accession
numbers: first character a letter, the remainder digits). The primary
(first) accession number occupies positions 13 to 18; subsequent
accession numbers occupy positions 20 to 25, 27 to 32, 34 to 39, 41 to
46, 48 to 53, 55 to 60, 62 to 67, and 69 to 74. No punctuation occurs
between accession numbers or after the final accession number;
accession numbers are separated only by one space.

3.5.7 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.

3.5.8 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.

3.5.9 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.

3.5.10 REFERENCE Format

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

  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 STANDARD line contains information about:

The degree to which the entry has been annotated:

`unannotated' for unannotated entries which include citation and
sequence only.

`simple' for unannotated entries which include the organism name and
protein coding regions as well as the citation and sequence.
 
`full' for fully annotated entries which include all the data items
that were described by the author.

The level of modification and review: 

`automatic' for data subjected only to automated (i.e., software) checks.

`staff_entry' for data that passed both automated and annotator checks.

`staff_review' for data that passed previous review levels as well as
a review by senior annotators and/or outside experts.

The format for the STANDARD line is: annotation degree <SPACE> review level

3.5.11 FEATURES Format

  GenBank releases use a new feature table format designed jointly by
GenBank, the EMBL Nucleotide Sequence Data Library, and the DNA Data
Bank of Japan. This format is now used by all three data banks.

  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 optional. However, a feature table must include one
header line and at least one feature descriptor line.

  The sections below provide a brief introduction to the new feature
table format. For a thorough description of the new feature table
format, see the document `The DDBJ/EMBL/GenBank Feature Table:
Definition.' If you would like a copy of this publication, contact
GenBank at the address shown on the front page of these Release Notes.

3.5.11.1 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.

allele		Related strain contains alternative gene form
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)
cellular	Region of cellular DNA
conflict	Independent determinations differ
D-loop      	Displacement loop
D_region	Span of the D immunological feature
enhancer	Cis-acting enhancer of promoter function
exon		Region that codes for part of spliced mRNA
GC_signal	`GC box' in eukaryotic promoters
iDNA		Intervening DNA eliminated by recombination
insertion_seq	Insertion sequence (IS), a small transposon
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 	A mutation alters the sequence here
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
provirus	Proviral sequence
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
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
virion		Virion (encapsidated) viral sequence
- (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)


3.5.11.2 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.

replace (location, location): The first location indicated should be
replaced by the sequence from the second location; used for
insertions, deletions, and variants.

3.5.11.3  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. Multiple citations are separated by commas (e.g.,
[1],[2],[3]).

  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 list of valid 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

/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 organism if different from that contained in
the entry's ORGANISM field

/partial	Differentiates between complete regions and partial ones

/phenotype	Phenotype conferred by the feature

/product	Name of a product encoded by the sequence

/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 coding region (automatically
generated)

/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

3.5.11.4 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.

3.5.11.5 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. In the sixth table entry, the replace operator is shown.

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        replace(258..258,"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


3.5.12 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).

3.5.13 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 exchanges data
with its international partners, EMBL and DDBJ, and incorporates all available
data in its releases and daily updates. NCBI distributes sequence data by
CD-ROM, anonymous FTP, and e-mail servers.  

  The electronic mail address for NCBI is:  info@ncbi.nlm.nih.gov
(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 data bank, should
be cited:

Benson, D., Lipman, D.J., and Ostell, J. GenBank. Nucl. Acids Res.
21(13):2963-2965 (1993)

  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 brackets
refer to one of the GenBank citations above and the REFERENCE in the
GenBank sequence entry.

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

(1) Benson, D. et al. Nucl. Acids Res. 21(13):2963-2965 (1993)
(2) Nellen, W. and Gallwitz, D. J. Mol. Biol. 159, 1-18 (1982)

6.4 GenBank Distribution Formats and Media

  GenBank data are available on industry-standard ISO-9660 CD-ROM.
The standard flat file format is included.  (Note: the floppy disk
format was discontinued at Rel. 71 and is NOT part of the NCBI CD-ROM.)

6.5 Other CD-ROM Titles

  This documentation accompanies the CD-ROM entitled, GenBank (Flat
File Format).  Each release is a full release incorporating all previous
GenBank data supplemented by new data from direct submissions, NCBI journal
scanning, and the EMBL and DDBJ DNA databases. No retrieval software is provided. 

  NCBI offers two other CD-ROMs.  Entrez: Sequences, contains the complete
information from GenBank Rel. 78.0 formatted to operate with an
included retrieval program, Entrez, for Macintosh and PC-compatible
computers running Microsoft Windows (3.1 or later).  The other CD-ROM
contains sequences and MEDLINE citations in a standard data description
language format, ASN.1.  Each of the three titles is in ISO 9660
format and is described in greater detail below. 

  The CD-ROMs are available by subscription through the Government
Printing Office (GPO).  U.S. prices are $76 for an annual subscription
to Entrez:Sequences/References and $47 for the each of the other disks.
An annual subscription will consist of six releases per year. Orders may be
submitted using the order form below for annual subscriptions.


Entrez: Sequences and Entrez: References

  Entrez: Sequences and Entrez: References are two CD-ROMs containing
molecular sequence and related bibliographic data with retrieval software.
Sequence data is integrated from a variety of sources, including
GenBank, EMBL, DDBJ, dbEST, PIR and SWISS-PROT. The bibliographic database
is on the second disk, Entrez: References, and consists of a sequence-related
subset of MEDLINE.  The DNA sequence, protein sequence and bibliographic data
are linked to provide easy traversal among the three databases. The retrieval
system allows for traditional keyword searching and uses pre-computed
statistical measures of relatedness to allow queries that will find all
articles or sequences similar to an article or sequence of interest.

  The Entrez disks contain retrieval software for the Macintosh and for
PC-compatible systems running Microsoft Windows (3.1 or later).  A minimum
of 2 Mbytes of memory is necessary. Documentation consists of a 30-page
user's guide for installation and operating instructions. (Source code
for an X11 version of the software for VMS and Unix platforms is
available through anonymous FTP from 'ncbi.nlm.nih.gov' in the
'entrez' directory.  Executables for several platforms are available on
an unsupported basis.)


NCBI-Sequences (ASN.1)

  This title provides the integrated sequence dataset used on the Entrez:
Sequences CD-ROM in the ISO ASN.1 standard data description format.
DNA and protein sequence data is incorporated, non-redundantly, from
GenBank, EMBL, DDBJ, Swiss-Prot and PIR and is linked to journal
citations appearing in MEDLINE. The MEDLINE subset currently consists
of approximately 50,000 citations. Files are provided which contain the
inter-document/sequence linkage information and indices to the byte
offsets of the beginning of sequence and bibliographic records. No
retrieval software is provided. 


Ordering Information  

  GPO handles all subscriptions and subscription-related questions. 
Telephone orders can be placed at (202) 783-3238.  Due to high
volume of telephone ordering, GPO encourages ordering by fax or
mail.  Quantity discounts of 25% are available for orders of 100 or
more CD-ROMs delivered to a single address.


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PRICES FOR INTERNATIONAL CUSTOMERS, INCLUDING AIR MAIL SERVICE FOR ONE YEAR

   Location                          Entrez:       NCBI        NCBI
                                     Sequences     GenBank     Sequences
   Zone 1.............................$87.74........$67.47......$67.47
     (South America)
   Zone 2.............................$97.94........$70.79......$70.79
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6.6 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. Please use the GenBank Error/Suggestion Report Form, which is
part of this distribution of GenBank (located in the file GBDAT.FRM),
to send your suggestions and corrections by electronic mail to:
update@ncbi.nlm.nih.gov or to the address on the error/suggestion form.
Please be certain to indicate the GenBank release number (e.g.,
Release 82.0) 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.

6.7  Acknowledgments

  NCBI acknowledges the contributions of the National Library of
Medicine's Library Operations Division in creating new sequence
entries for GenBank.  The following people are involved in the
addition of new sequence data from the literature and direct
author submissions:


NLM Library Operations Sequence Indexers

	Sally Davidson
	Michael Fetchko
	Fu-Sen Hu
	Min-Chi Huang
	Susan Krist
	Maureen Madden
	Lillian Riddick
	Nancy Sorden
	Jane Weisemann

ComputerCraft Support Contract at NCBI - Quality Assurance and Keyboarding

	Monika Momiyama
	Junga Kim
	Mehrnoush Janbakhsh Najafabadi
	Shirley Meyers
	Ken Geter
	Irene Fang
	Jenny Wang
	Tracy Lou

Management Systems Designers Contract Support - Data Flow

	Francis Ouellette


6.8 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 and accept no responsibility for
any consequences of the receipt or use of the information.


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

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