[Genbank-bb] GenBank Release 163.0 Now Aailable

Mark Cavanaugh via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Sat Dec 22 16:56:45 EST 2007


Greetings GenBank Users,

  GenBank Release 163.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 163.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 163.0

  Close-of-data for GenBank 163.0 occured on 12/17/2007. Uncompressed, the
Release 163.0 flatfiles require roughly 314 GB (sequence files only)
or 335 GB (including the 'short directory', 'index' and the *.txt files). 
The ASN.1 data require approximately 289 GB.

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

  Release  Date       Base Pairs   Entries

  162      Oct 2007   81563399765  77632813
  163      Dec 2007   83874179730  80388382

Recent statistics for WGS sequences:

  Release  Date       Base Pairs   Entries

  162      Oct 2007  102003045298  25354041
  163      Dec 2007  106505691578  26177471

  During the 59 days between the close dates for GenBank Releases 162.0 and
163.0, the non-WGS/non-CON portion of GenBank grew by 2,310,779,965 basepairs
and by 2,755,569 sequence records. During that same period, 655,660 records
were updated. An average of about 57,800 non-WGS records were added
and/or updated per day.

  Between releases 162.0 and 163.0, the WGS portion of GenBank grew by
4,502,646,280 basepairs and 823,430 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 163.0 and Upcoming Changes) have been appended
below.
		** Important Note **

  GenBank 'index' files are now provided without any EST content, and without
most GSS content. See Section 1.3.9 of the release notes for further details.
NCBI is considering ceasing support for the index files, so we encourage
affected users to review that section and provide feedback.

  Release 163.0 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: December 15 2007, 163.0). 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 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
163.0, please send email outlining your difficulties to:

        info from ncbi.nlm.nih.gov

Mark Cavanaugh, Vladimir Alekseyev, Michael Kimelman
GenBank
NCBI/NLM/NIH/HHS



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