[Genbank-bb] GenBank Release 164.0 Now Aailable

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Tue Feb 19 01:17:39 EST 2008


Greetings GenBank Users,

  GenBank Release 164.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 164.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 164.0

  Close-of-data for GenBank 164.0 occured on 02/12/2008. Uncompressed, the
Release 164.0 flatfiles require roughly 321 GB (sequence files only)
or 342 GB (including the 'short directory', 'index' and the *.txt files). 
The ASN.1 data require approximately 295 GB.

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

  Release  Date       Base Pairs   Entries

  163      Dec 2007   83874179730  80388382
  164      Feb 2008   85759586764  82853685

Recent statistics for WGS sequences:

  Release  Date       Base Pairs   Entries

  163      Dec 2007  106505691578  26177471
  164      Feb 2008  108635736141  27439206

  During the 56 days between the close dates for GenBank Releases 163.0 and
164.0, the non-WGS/non-CON portion of GenBank grew by 1,885,407,034 basepairs
and by 2,465,303 sequence records. During that same period, 1,750,703 records
were updated. An average of about 75,286 non-WGS/non-CON records were added
and/or updated per day.

  Between releases 163.0 and 164.0, the WGS component of GenBank grew by
2,130,044,563 basepairs and by 1,261,735 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 164.0 and Upcoming Changes) have been appended
below.
                ** Important Notes **

  A new GenBank division will become legal as of Release 165.0 in April 2008:
the Transcriptome Shotgun Assembly, or TSA, division. Please see Section 1.4.1
of the release notes for more information about TSA and the records that it 
will contain.

  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 164.0 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: February 15 2008, 164.0). 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
164.0, 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 164.0

1.3.1 Organizational changes

  The total number of sequence data files increased by 10 with this release:

  - the CON division is now comprised of  85 files (+1)
  - the ENV division is now comprised of   8 files (+1)
  - the HTC division is now comprised of  13 files (+1)
  - the EST division is now comprised of 694 files (+19)
  - the GSS division is now comprised of 277 files (-18)   (see Note below)
  - the HTG division is now comprised of 107 files (+2)
  - the INV division is now comprised of  12 files (+1)
  - the PAT division is now comprised of  35 files (+1)
  - the PLN division is now comprised of  28 files (+1)
  - the PRI division is now comprised of  35 files (+1)

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

  - the AUT (AUTHOR Name) index is now comprised of 50 files (+2)

  NOTE:

  A configuration setting that determines the average size for many
  of the GSS division GenBank flatfiles was mistakenly changed for
  Release 163.0. This resulted in a filesize decrease for a large
  number of GSS flatfiles, from 230 MB to 210 MB. Consequently, the
  total number of GSS flatfiles underwent an artificially-large
  increase of 26 files.

  The configuration setting was restored for GenBank Release 164.0.
  As as a result, there is now an apparent net decrease of 18 GSS files.
  Our apologies for any confusion that this may have caused.
   
1.3.2 Divisional protein FASTA files now available

  Individual protein FASTA data files are now being made available for
GenBank releases, in the ASN.1 area of the NCBI FTP site:

        ftp://ftp.ncbi.nih.gov/ncbi-asn1/protein_fasta

Each protein FASTA file reflects the protein data content of the ASN.1
data file bearing the same division code in its name. For example, these
two "pri12" divisional files:

        gbpri12.aso.gz
        gbpri12.fsa_aa.gz

are 'equivalent', in that the proteins annotated on the DNA sequences
of gbpri12.aso are all present in gbpri12.fsa_aa.gz . For further
information, please see this README:

        ftp://ftp.ncbi.nih.gov/ncbi-asn1/protein_fasta/README.protein_fasta

  These divisional files are a replacement (see Section 1.4.2) for the single
protein FASTA file that has been provided in conjunction with GenBank releases:

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

where 'NNN' represents a three-digit GenBank release number.

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-one of the GSS flatfiles in Release 164.0. Consider gbgss227.seq :


GBGSS1.SEQ           Genetic Sequence Data Bank
                          February 15 2008

                NCBI-GenBank Flat File Release 164.0

                           GSS Sequences (Part 1)

   86927 loci,    64285938 bases, from    86927 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "227" 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 New GenBank TSA division: Transcriptome Shotgun Assembly

  A new GenBank division for assembled mRNA sequences, Transcriptome Shotgun
Assembly (TSA), will be included in GenBank releases on or after Release 165.0
in April of 2008.

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" will be present for 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.

  TSA records make use of the same PRIMARY block that is utilized for
Third-Party Annotation (TPA) records. The PRIMARY block will contain
references to the underlying reads/transcripts that were assembled to
construct the 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.

1.4.2 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



More information about the Genbankb mailing list