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[Genbank-bb] GenBank Release 207.0 Available : April 16 2015

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Thu Apr 16 20:41:08 EST 2015


Greetings GenBank Users,

  GenBank Release 207.0 is now available via FTP from the National Center
for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 207.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 207.0

  Close-of-data for GenBank 207.0 occurred on 04/13/2015. Uncompressed,
the Release 207.0 flatfiles require roughly 709 GB (sequence files only).
The ASN.1 data require approximately 580 GB.

Recent statistics for 'traditional' sequences (non-WGS, non-CON, non-TSA):

  Release  Date      Base Pairs    Entries

  206      Feb 2015  187893826750  181336445
  207      Apr 2015  189739230107  182188746

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  206    Feb 2015   873281414087   205465046
  207    Apr 2015   969102906813   243779199

Recent statistics for TSA sequences:

  206    Feb 2015    49765340047    66706014
  207    Apr 2015    55796332435    71989588

  During the 59 days between the close dates for GenBank Releases 206.0
and 207.0, the 'traditional' portion of GenBank grew by 1,845,403,357
basepairs and by 852,301 sequence records. During that same period,
166,863 records were updated. An average of 17,274 'traditional' records
were added and/or updated per day.

  Between releases 206.0 and 207.0, the WGS component of GenBank grew by
95,821,492,726 basepairs and by 38,314,153 sequence records.

  Between releases 206.0 and 207.0, the TSA component of GenBank grew by
6,030,992,388 basepairs and by 5,283,574 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 207.0 and Upcoming Changes) have been appended
below for your convenience.

                    * * * Important * * *

  A significant change is described in Section 1.4.1 of the release
notes: an anticipated phasing-out of NCBI GI sequence identifiers.
Users who make use of GIs in their information systems and analysis
pipelines should take particular note of that section.

  Release 207.0 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 2015, 207.0). 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
207.0, 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 207.0

1.3.1 Organizational changes

The total number of sequence data files increased by 36 with this release:

  - the BCT division is now composed of 178 files (+9)
  - the CON division is now composed of 317 files (+14)
  - the ENV division is now composed of  81 files (+1)
  - the EST division is now composed of 478 files (+1)
  - the HTG division is now composed of 142 files (+1)
  - the INV division is now composed of 126 files (-7)
  - the PAT division is now composed of 219 files (+2)
  - the PLN division is now composed of 107 files (+11)
  - the TSA division is now composed of 175 files (+3)
  - the VRL division is now composed of  34 files (+1)

  The decrease in the number of INV division sequence files is due to
the suppression of 20,145 records (LM656229-LM676373) with a total of
1.28 gigabases of sequence data. They were determined to be redundant
with scaffolds associated with the CCMX01 WGS project : LN627018-LN647175

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 125
of the GSS flatfiles in Release 207.0. Consider gbgss169.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                           April 15 2015

                NCBI-GenBank Flat File Release 207.0

                           GSS Sequences (Part 1)

   87051 loci,    63867441 bases, from    87051 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "169" 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 GI sequence identifiers to be phased out (slowly!) at NCBI

  The numeric GI sequence identifier that NCBI assigns to all nucleotide
and protein sequences was first introduced for GenBank Release products
as of GenBank 81.0, in February 1994. See:

     ftp://ftp.ncbi.nih.gov/genbank/release.notes/gb81.release.notes

 These simple, uniform, integer-based unique identifiers (which predated the
introduction of Accession.Version sequence identifiers) were crucial to the
development of NCBI's Entrez retrieval system, and have served their purpose
very well for nearly 20 years. 

  However, as NCBI considers how best to address the expected increase in the
volume of submitted sequence data, it is clear that prior practices will need
to be re-thought. As an example, imagine 100,000 pathogen-related
genomes/samples, each with 5000 proteins, most of which are common to all. We
will be moving toward solutions that represent each unique protein *once*.
The coding region protein products for each genome will likely continue to be
assigned their own Accession.Version identifiers, but (within the NCBI data
model) they will simply *reference* the unique proteins. And, they will no
longer be issued GIs of their own.

  Such a change will likely have a significant impact on NCBI users who utilize
GIs in their own information systems and analysis pipelines, so it will not be
introduced quickly. You can expect that a great deal of additional detail will
be made available via NCBI's various announcement mechanisms.

  *This* particular announcement is chiefly intended to provide some advance
warning to our users. There _are_ classes of GenBank sequences that are not
being assigned GIs. If GIs are central to your operations, then it might be
appropriate to begin planning a switch to the use of Accession.Version
identifiers instead.

  NCBI now has several WGS submissions for which GIs have not been assigned,
for both the contigs and the scaffolds. As an example, here are excerpts of
the flatfile representation for the first ALWZ04 (the fourth assembly-version
of the ALWZ project) contig, and the 'singleton scaffold' which is constructed
from it:

LOCUS       ALWZ040000001           1191 bp    DNA     linear   PLN 13-MAR-2015
DEFINITION  Picea glauca, whole genome shotgun sequence.
ACCESSION   ALWZ040000001 ALWZ040000000
VERSION     ALWZ040000001.1
DBLINK      BioProject: PRJNA83435
            BioSample: SAMN01120252
....
ORIGIN      
        1 ctataatacc cctatgccaa acgaacccaa ttgtaaatgt aaatgcaaat gtacttaggc
       61 tggttagttg tttaatatca ttttttgtat gcaccttcca tggtataatg cgcacatgta
      121 tagcgcacta aaattatgaa gtgtgcccat tccaagatat tgcgcgtaaa aaacttaagt
      181 gtgcatgatt ttgagactag ggagactttg tgtatatgtt gtgttttata tgctggagag
      241 acaattatta ttagttagga ggattatgtt ttgtactagg caagagagcc tagatgttaa
      301 aggctagtga gcctattttt gtatatgtct catcattaat ataatacatc attgtgtgta
      361 gaccgaccat gataaaagag tatgggggac taaactccac tagttaggga aaaggggcgc
      421 taaaatttaa ggaaaatggc taagataggg aacttaagcc aaaaaggaat attatattaa
      481 tattccttaa agtataaagt atggataatt attttatcct aagttagaag gatgtggaca
      541 agtgggccaa agtagctccc aacatgacag gtgtcaagtt gggaacatgc atacatatag
      601 gttggactta gttcattttc ctaacgattc catcatcatt caaacactca ttgatctatc
      661 ctccatacct ccttgtacct agatccgtac ctgaaccaaa accatactcg tgcatataca
      721 tgtacttgta cctagttatc ttgggagata gactaaagaa gcgagttgtt aggcccatgg
      781 gatattgaag aggtaggctt tcaggcccgt gggatattga agaggcaggt tttcaagccc
      841 atgggatatt gaagaggtgg gttgtcaagc ccatgataaa tttctctctc ggtgagggaa
      901 ttgttgggaa ttgatttcct gaatgtgtta aactgcattg atagggatct gagaattcct
      961 ttctggccta ttgctgaagc tttggaaggg aggtggggca accgagggac tgttgagaag
     1021 agaagggtca cacttcctgg ggtgggacaa gcatgtgggg aattagggat tgcaggatgt
     1081 tagtttgaat tggcacctat gacagagtct ttcctattgt ctgagatatg tcagcttggt
     1141 taggaaaccc tttacctggg tagagtttag tcccagctcg ggggtgaccc a
//

LOCUS       ALWZ04S0000001          1191 bp    DNA     linear   CON 13-MAR-2015
DEFINITION  Picea glauca Pg-01r141201s0000001, whole genome shotgun sequence.
ACCESSION   ALWZ04S0000001 ALWZ0400000000
VERSION     ALWZ04S0000001.1
DBLINK      BioProject: PRJNA83435
            BioSample: SAMN01120252
....
CONTIG      join(ALWZ040000001.1:1..1191)
//


**Note the absence of a GI value on the VERSION line of these two records**

Sample URLs from which ALWZ04 data may be obtained include:

  http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ALWZ04#contigs
  http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ALWZ04#scaffolds

  http://www.ncbi.nlm.nih.gov/Traces/wgs/?download=ALWZ04.gbff.1.gz
  http://www.ncbi.nlm.nih.gov/Traces/wgs/?download=ALWZ04S.gbff.1.gz

  ftp://ftp.ncbi.nlm.nih.gov/genbank/wgs/wgs.ALWZ.*.gbff.gz
  ftp://ftp.ncbi.nlm.nih.gov/genbank/wgs/wgs.ALWZ.scflds.*.gbff.gz

Unannotated WGS projects consisting of many millions of contigs and 
scaffolds represent the first class of records for which GIs are no
longer being assigned. But the practice will ultimately expand to
include other classes of records.





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