Greetings GenBank Users,
GenBank Release 195.0 is now available via FTP from the
National Center for Biotechnology Information (NCBI):
Ftp Site Directory Contents
---------------- --------- ---------------------------------------
ftp.ncbi.nih.gov genbank GenBank Release 195.0 flatfiles
ncbi-asn1 ASN.1 data used to create Release 195.0
Close-of-data for GenBank 195.0 occurred on 04/11/2013. Uncompressed,
the Release 195.0 flatfiles require roughly 594 GB (sequence files only).
The ASN.1 data require approximately 490 GB.
Recent statistics for non-WGS, non-CON sequences:
Release Date Base Pairs Entries
194 Feb 2013 150141354858 162886727
195 Apr 2013 151178979155 164136731
Recent statistics for WGS sequences:
Release Date Base Pairs Entries
194 Feb 2013 390900990416 103101291
195 Apr 2013 418026593606 110509314
During the 57 days between the close dates for GenBank Releases 194.0
and 195.0, the non-WGS/non-CON portion of GenBank grew by 1,037,624,297
basepairs and by 1,250,004 sequence records. During that same period,
628,961 records were updated. An average of 32,964 non-WGS/non-CON
records were added and/or updated per day.
Between releases 194.0 and 195.0, the WGS component of GenBank grew by
27,125,603,190 basepairs and by 7,408,023 sequence records.
For additional release information, see the README files in either of
the directories mentioned above, and the release notes (gbrel.txt) in
the genbank directory. Sections 1.3 and 1.4 of the release notes
(Changes in Release 195.0 and Upcoming Changes) have been appended
below for your convenience.
Release 195.0 data, and subsequent updates, are available now via
NCBI's Entrez and Blast services.
As a general guideline, we suggest first transferring the GenBank
release notes (gbrel.txt) whenever a release is being obtained. Check
to make sure that the date and release number in the header of the
release notes are current (eg: April 15 2013, 195.0). If they are
not, interrupt the remaining transfers and then request assistance from
the NCBI Service Desk.
A comprehensive check of the headers of all release files after your
transfers are complete is also suggested. Here's how one might go about
this on a Unix or Linux platform, using csh/tcsh :
set files = `ls gb*.*`
foreach i ($files)
head -10 $i | grep Release
end
Or, if the files are compressed, perhaps:
gzcat $i | head -10 | grep Release
If you encounter problems while ftp'ing or uncompressing Release
195.0, please send email outlining your difficulties to:
info from ncbi.nlm.nih.gov
Mark Cavanaugh, Michael Kimelman, Ilya Dondoshansky, Sergey Zhdanov
GenBank
NCBI/NLM/NIH/HHS
1.3 Important Changes in Release 195.0
1.3.1 Organizational changes
The total number of sequence data files increased by 30 with this release:
- the BCT division is now composed of 100 files (+2)
- the CON division is now composed of 205 files (+18)
- the ENV division is now composed of 60 files (+1)
- the EST division is now composed of 472 files (+3)
- the PHG division is now composed of 2 files (+1)
- the PLN division is now composed of 61 files (+1)
- the TSA division is now composed of 141 files (+3)
- the VRL division is now composed of 25 files (+1)
1.3.2 Release Catalog data files have replaced old "index" files
As described in the February 2013 release notes for GenBank 194.0,
the legacy "index" files that previously accompanied the sequence
data files of GenBank releases have been discontinued. They have
been replaced by new "release catalog" products.
Each GenBank sequence record in the new catalog files is represented
by a 10-field, TAB-delimited row of data. The data fields are:
Accession Number
Accession.Version
NCBI GI Identifier (if assigned)
Molecule Type (dna, rna, mrna, etc)
Sequence Length
Organism Name
NCBI Taxonomy Database Identifier
Division Code
BioProject Accession Number
BioSample Accession Number
When a value does not exist for one of these fields, the field in the catalog
will be empty (eg, two sequential TAB characters can be present, with
nothing between them). Here is an example of the catalog data for CP003933:
CP003933 CP003933.1 429549985 dna 3618794 Sinorhizobium meliloti GR4 1235461 BCT PRJNA175860
It is our hope that the release catalog will be more useful than the old
accession number index files (gbacc*.idx).
The author-name (gbaut*.idx), journal (gbjou*.idx), keyword (gbkey*.idx)
and secondary-accession (gbsec*.idx) index files have been discontinued
without replacements.
However, new "PMID List" and "Gene List" TAB-delimited files will accompany
the release catalog. The format of the PubMed Identifier List is:
Accession1 Accession1.Version PMID-1,PMID-2,PMID-3,.....
Accession2 Accession2.Version PMID-1,PMID-2,PMID-3,.....
....
And the format of the Gene List is:
Accession1 Accession1.Version Gene-Symbol-1 Locus-Tag-1
Accession1 Accession1.Version Gene-Symbol-2 Locus-Tag-2
Accession1 Accession1.Version Gene-Symbol-3 Locus-Tag-3
Accession2 Accession2.Version Gene-Symbol-1 Locus-Tag-1
Accession2 Accession2.Version Gene-Symbol-2 Locus-Tag-2
Accession2 Accession2.Version Gene-Symbol-3 Locus-Tag-3
....
Note that either Gene Symbol or Locus Tag could be null for any given
gene.
The "Short Directory" files (gbsdr*.txt), which provided the accession
and definition line (often truncated) for all sequence records, has been
discontinued without a replacement.
The release catalog and accompanying lists are provided via files that
are specific to EST, GSS, and non-EST/GSS (everything else). The catalogs
and lists do not currently include the contig sequence records for WGS
projects. The files are made available in a new sub-directory of the
GenBank FTP area:
genbank/catalog
And their names are:
gb195.est.catalog.txt.gz
gb195.gss.catalog.txt.gz
gb195.other.catalog.txt.gz
gb195.est.pmid_list.txt.gz
gb195.gss.pmid_list.txt.gz
gb195.other.pmid_list.txt.gz
gb195.gss.gene_list.txt.gz
gb195.other.gene_list.txt.gz
Note that there is no Gene List for EST sequences. This is because
EST records in GenBank have no annotation other than source features.
Our goal is to provide companion products for the release files which will
be of help for large-scale consumers of GenBank data. To that end, if you
have ideas for how to make the release catalog more useful, or have
suggestions for additional companion files like the PMID and Gene lists,
please let us know by contacting the NCBI Help Desk : info from ncbi.nlm.nih.gov .
Be aware that these products are still fairly new. If you encounter
problems with their content, we would appreciate your feedback (again,
via the NCBI Help Desk).
1.3.3 GSS File Header Problem
GSS sequences at GenBank are maintained in two different systems, depending
on their origin, and the dumps from those systems occur in parallel. Because
the second dump (for example) has no prior knowledge of exactly how many GSS
files will be dumped by the first, it does not know how to number its own
output files.
There is thus a discrepancy between the filenames and file headers for 115
of the GSS flatfiles in Release 195.0. Consider gbgss156.seq :
GBGSS1.SEQ Genetic Sequence Data Bank
April 15 2013
NCBI-GenBank Flat File Release 195.0
GSS Sequences (Part 1)
87092 loci, 63917090 bases, from 87092 reported sequences
Here, the filename and part number in the header is "1", though the file
has been renamed as "156" based on the number of files dumped from the other
system. We hope to resolve this discrepancy at some point, but the priority
is certainly much lower than many other tasks.
1.4 Upcoming Changes
No changes impacting the flatfile format are expected between the
April 2013 and June 2013 GenBank releases.
