[Genbank-bb] GenBank Release 165.0 Now Aailable

Mark Cavanaugh via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Fri Apr 18 15:52:46 EST 2008


Greetings GenBank Users,

  GenBank Release 165.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 165.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 165.0

  Close-of-data for GenBank 165.0 occured on 04/15/2008. Uncompressed, the
Release 165.0 flatfiles require roughly 332 GB (sequence files only)
or 353 GB (including the 'short directory', 'index' and the *.txt files). 
The ASN.1 data require approximately 305 GB.

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

  Release  Date       Base Pairs   Entries

  164      Feb 2008   85759586764  82853685
  165      Apr 2008   89172350468  85500730

Recent statistics for WGS sequences:

  Release  Date       Base Pairs   Entries

  164      Feb 2008  108635736141  27439206
  165      Apr 2008  110500961400  26931049

  During the 62 days between the close dates for GenBank Releases 164.0 and
165.0, the non-WGS/non-CON portion of GenBank grew by 3,412,763,704 basepairs
and by 2,647,045 sequence records. During that same period, 1,590,201 records
were updated. An average of about 68,340 non-WGS/non-CON records were added
and/or updated per day.

  Between releases 164.0 and 165.0, the WGS component of GenBank grew by
1,865,225,259 basepairs. The number of records decreased by 508,157 due to
the re-assembly of WGS project AAKN, into far fewer (but larger) contigs.

  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 165.0 and Upcoming Changes) have been appended
below.
                ** Important Notes **

*  A new GenBank division has become legal with this April's Release 165.0 :
   the Transcriptome Shotgun Assembly, or TSA, division. Please see
   Section 1.3.2 of the release notes for more information about TSA and the
   records that it will contain.

*  Support for the single, comprehensive protein FASTA file which accompanies
   GenBank releases will be ceased as of the June 2008 release. See Section
   1.4.1 of the release notes for details.

*  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 165.0 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 2008, 165.0). 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
165.0, please send email outlining your difficulties to:

        info from ncbi.nlm.nih.gov

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


1.3 Important Changes in Release 165.0

1.3.1 Organizational changes

  The total number of sequence data files increased by 41 with this release:

  - the BCT division is now comprised of  28 files (+2)
  - the EST division is now comprised of 713 files (+19)
  - the GSS division is now comprised of 285 files (+8)
  - the HTG division is now comprised of 114 files (+7)
  - the PAT division is now comprised of  38 files (+3)
  - the PLN division is now comprised of  29 files (+1)
  - the VRL division is now comprised of   9 files (+1)

1.3.2 New Transcriptome Shotgun Assembly (TSA) division now legal

  A new GenBank division for assembled mRNA sequences, Transcriptome Shotgun
Assembly (TSA), can now appear in GenBank releases, as of this April 2008
Release 165.0. The date of first appearance of a TSA record will depend
on the status of TSA submission processing, but it *is* expected that they will
begin to appear in the GenBank Incremental Updates (GIU) within the next
month, and that Release 166.0 will include a divisional TSA file.

Files in this new division will have filenames of:

	gbtsaNN.aso.gz	(ASN.1 format)
	gbtsaNN.seq.gz	(GenBank flatfile format)

where 'NN' represents an integer file-number within the TSA division.

  TSA sequences are shotgun assemblies of primary sequences deposited in
dbEST, the Trace Archive (TA) or the Short-Read Archive (SRA).  Keywords
"TSA" and "Transcriptome Shotgun Assembly" are present on all TSA
records, in addition to a division code value of "TSA" on the LOCUS line.

  No format changes (new or changed line types, features, or qualifiers)
are anticipated for this new class of GenBank record.

  However, note that TSA records make use of the same PRIMARY block that
is utilized for Third-Party Annotation (TPA) records. The PRIMARY block
contains references to the underlying reads/transcripts that were assembled
to construct a TSA record.

  It might be helpful to review Third Party Annotation record BK005658,
which provides a good example of PRIMARY block usage:

	http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=83843278

Requirements for the new Transcriptome Shotgun Assembly division include:

1. Submission of primary transcipt sequence data to dbEST, the Trace Archive,
   or the Short-Read archive (SRA).  

2. Registration of an associated transcriptome project with the International
   Nucleotide Sequence Database Collaboration (INSDC).

   For information about submitting projects via NCBI/GenBank, see:

	http://www.ncbi.nlm.nih.gov/genomes/mpfsubmission.cgi

3. Submission of TSA sequence records to GenBank, including an assembly file
   (.ace format)

Note that TSA records and the primary transcript sequences that they are
built from must be provided by the same submitter or collaborative group.

Examples of TSA records and more information about how to submit them
will be provided in future editions of these release notes, and via the
GenBank newsgroup.

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
unsorted.

  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
fifty-four of the GSS flatfiles in Release 165.0. Consider gbgss232.seq :

GBGSS1.SEQ           Genetic Sequence Data Bank
                           April 15 2008

                NCBI-GenBank Flat File Release 165.0

                           GSS Sequences (Part 1)

   87177 loci,    64476488 bases, from    87177 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "232" based on the number of files dumped from the other
system.  We will work to resolve this discrepancy in future releases, but the
priority is certainly much lower than many other tasks.

1.4 Upcoming Changes

1.4.1 Comprehensive protein FASTA file to be discontinued

  With the availability of divisional protein FASTA files as of GenBank
Release 164.0, support for the single, large, comprehensive protein FASTA
file:

	ftp://ftp.ncbi.nih.gov/genbank/relNNN.fsa_aa.gz

(where 'NNN' represents a three-digit GenBank release number) will be
discontinued after GenBank Release 166.0 in June of 2008. The size
of this file has grown to exceed 4GB, which is unmanageable for many users.

  Users are advised to make plans to utilize the new divisional files by
August of 2008. If this timetable poses problems, please let us know at the
NCBI Service Desk:

	info from ncbi.nlm.nih.gov



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