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[Genbank-bb] GenBank Release 196.0 Available : June 17 2013

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Mon Jun 17 15:55:20 EST 2013


Greetings GenBank Users,

  GenBank Release 196.0 is now available via FTP from the
National Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 196.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 196.0

  Close-of-data for GenBank 196.0 occurred on 06/13/2013. Uncompressed,
the Release 196.0 flatfiles require roughly 600 GB (sequence files only).
The ASN.1 data require approximately 495 GB.

Recent statistics for non-WGS, non-CON sequences:

  Release  Date      Base Pairs    Entries

  195      Apr 2013  151178979155  164136731
  196      Jun 2013  152599230112  165740164

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  195    Apr 2013  418026593606  110509314
  196    Jun 2013  453829752320  112488036

  During the 63 days between the close dates for GenBank Releases 195.0
and 196.0, the non-WGS/non-CON portion of GenBank grew by 1,420,250,957
basepairs and by 1,603,433 sequence records. During that same period,
590,119 records were updated. An average of 34,818 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 194.0 and 196.0, the WGS component of GenBank grew by
35,803,158,714 basepairs and by 1,978,722 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 196.0 and Upcoming Changes) have been appended
below for your convenience.

  Release 196.0 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: June 15 2013, 196.0). 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
196.0, 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 196.0

1.3.1 Organizational changes

The total number of sequence data files increased by 19 with this release:

  - the BCT division is now composed of 103 files (+3)
  - the CON division is now composed of 208 files (+3)
  - the ENV division is now composed of  61 files (+1)
  - the EST division is now composed of 473 files (+1)
  - the GSS division is now composed of 273 files (+3)
  - the INV division is now composed of  35 files (+1)
  - the PAT division is now composed of 195 files (+5)
  - the PLN division is now composed of  62 files (+1)
  - the ROD division is now composed of  31 files (+1)

1.3.2 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 196.0. Consider gbgss159.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                            June 15 2013

                NCBI-GenBank Flat File Release 196.0

                           GSS Sequences (Part 1)

   87041 loci,    63875698 bases, from    87041 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "159" 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
June 2013 and October 2013 GenBank releases.






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