[Genbank-bb] GenBank Release 175.0 Now Available

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Fri Dec 18 15:18:27 EST 2009

Greetings GenBank Users,

  GenBank Release 175.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 175.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 175.0

  Close-of-data for GenBank 175.0 occurred on 12/15/2009. Uncompressed,
the Release 175.0 flatfiles require roughly 422 GB (sequence files only)
or 452 GB (including the 'short directory', 'index' and the *.txt
files). The ASN.1 data require approximately 381 GB.

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

  Release  Date      Base Pairs    Entries

  174      Oct 2009  108560236506  110946879
  175      Dec 2009  110118557163  112910950

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  174      Oct 2009  149348923035  48119301
  175      Dec 2009  158317168385  54076973

  During the 60 days between the close dates for GenBank Releases 174.0
and 175.0, the non-WGS/non-CON portion of GenBank grew by 1,558,320,657
basepairs and by 1,964,071 sequence records. During that same period,
1,873,102 records were updated. An average of about 63,900 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 174.0 and 175.0, the WGS component of GenBank grew by
8,968,245,350 basepairs and by 5,957,672 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 175.0 and Upcoming Changes) have been appended
below for your convenience.

                ** Important Notes **

*  The average uncompressed size of EST and GSS sequence files will
   be doubled to about 500MB for the February 2010 release. See
   Section 1.4.1 of the release notes for more information.

*  GenBank 'index' files are now provided without any EST content, and
   without most GSS content. See Section 1.3.3 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 175.0 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 2009, 175.0). 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
175.0, 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 175.0

1.3.1 Organizational changes

The total number of sequence data files increased by 24 with this release:

  - the BCT division is now composed of  50 files (+2)
  - the CON division is now composed of 130 files (-2)
  - the ENV division is now composed of  23 files (+1)
  - the EST division is now composed of 904 files (+12)
  - the GSS division is now composed of 356 files (+6)
  - the PAT division is now composed of  88 files (+3)
  - the PLN division is now composed of  39 files (+1)
  - the PRI division is now composed of  41 files (+1)

  The change in the number of CON division files reflects a decrease
  in the number of records that are constructed from WGS projects.
  Re-assembly of WGS projects can sometimes result in fewer (but larger)
  contigs, and hence the number of CON-division scaffolds built from 
  the contigs can also decrease.

The total number of 'index' files increased by 2 with this release:

  - the AUT (author) index is now composed of 71 files (+2)

1.3.2 /artificial_location qualifier introduced

  A new qualifier, intended for use in limited genome-scale annotation
contexts, is now legal as of this December 2009 GenBank Release 175.0 :

Qualifier       /artificial_location
Definition      indicates that location of the CDS or mRNA is modified to adjust
                for the presence of a frameshift or internal stop codon and not
                because of biological processing between the regions.
Value format    none
Example         /artificial_location
Comment         expected to be used only for genome-scale annotation, either
                because a heterogeneous population was sequenced or because the
                feature is in a region of low-quality sequence.

1.3.3 Changes in the content of index files

  As described in the GB 153 release notes, the 'index' files which accompany
GenBank releases (see Section 3.3) are considered to be a legacy data product by
NCBI, generated mostly for historical reasons. FTP statistics of January 2005
seem to support this: the index files were transferred only half as frequently as
the files of sequence records. The inherent inefficiencies of the index file
format also lead us to suspect that they have little serious use by the user
community, particularly for EST and GSS records.

  The software that generated the index file products received little
attention over the years, and finally reached its limitations in
February 2006 (Release 152.0). The required multi-server queries which
obtained and sorted many millions of rows of terms from several different
databases simply outgrew the capacity of the hardware used for GenBank
Release generation.

  Our short-term solution is to cease generating some index-file content
for all EST sequence records, and for GSS sequence records that originate
via direct submission to NCBI.

  The three gbacc*.idx index files continue to reflect the entirety of the
release, including all EST and GSS records, however the file contents are

  These 'solutions' are really just stop-gaps, and we will likely pursue
one of two options:

a) Cease support of the 'index' file products altogether.

b) Provide new products that present some of the most useful data from
   the legacy 'index' files, and cease support for other types of index data.

  If you are a user of the 'index' files associated with GenBank releases, we
encourage you to make your wishes known, either via the GenBank newsgroup,
or via email to NCBI's Service Desk:

   info from ncbi.nlm.nih.gov

  Our apologies for any inconvenience that these changes may cause.

1.3.4 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
eighty-two of the GSS flatfiles in Release 175.0. Consider gbgss275.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                        December 15 2009

                NCBI-GenBank Flat File Release 175.0

                           GSS Sequences (Part 1)

   87171 loci,    64182194 bases, from    87171 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "275" 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

1.4.1 Increase in the size of EST and GSS sequence files

  The average size of EST and GSS sequence files, uncompressed, is
approximately 222 MB. For the February 2010 GenBank release, we will
increase the average file size to about 500 MB, which would reduce
the number of EST/GSS files by about 50% (from roughly 1200 to about 600).

  This change should make FTP transfers of an entire release easier to
manage (fewer files), while still maintaining a tractable uncompressed
file size. 

1.4.2 New /pseudogene and /non_functional qualifiers

  The GenBank 173.0 release notes described an anticipated conversion
of the /pseudo qualifer to /non_functional, based on the results of
the May 2009 INSDC annual meeting:

    "Because the term "pseudo" is often assumed to mean 'pseudogene',
     the /pseudo qualifier will be renamed as /non_functional, to
     better reflect its actual usage in the sequence databases."

  During follow-up discussions, the INSDC members decided that existing
uses of /pseudo can include both of the possible meanings of the term,
and that a more conservative course would be to introduce two new


  Sequence submission tools will be updated to utilize these, and
the ambiguous /pseudo qualifier will be deprecated. If it is 
possible, existing instances of /pseudo would then be converted
to one of the two new qualifiers.

  /pseudogene and /non_functional will become legal for the Feature
Table as of the April 2010 GenBank Release.

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