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[Genbank-bb] GenBank Release 195.0 Available : April 15 2013 [Re-sent Friday April 19]

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Fri Apr 19 14:27:54 EST 2013

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

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

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
	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

  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:


And their names are:




  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.

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