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[Genbank-bb] GenBank Release 202.0 Available : June 16 2014

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Mon Jun 16 19:53:17 EST 2014


Greetings GenBank Users,

  GenBank Release 202.0 is now available via FTP from the National Center
for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 202.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 202.0

  Close-of-data for GenBank 202.0 occurred on 06/12/2014. Uncompressed,
the Release 202.0 flatfiles require roughly 642 GB (sequence files only).
The ASN.1 data require approximately 538 GB.

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

  Release  Date      Base Pairs    Entries

  201      Apr 2014  159813411760  171744486
  202      Jun 2014  161822845643  173353076

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  201    Apr 2014  621015432437  143446790
  202    Jun 2014  719581958743  175779064

  During the 60 days between the close dates for GenBank Releases 201.0
and 202.0, the non-WGS/non-CON portion of GenBank grew by 2,009,433,883
basepairs and by 1,608,590 sequence records. During that same period,
564,904 records were updated. An average of 36,225 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 201.0 and 202.0, the WGS component of GenBank grew by
98,566,526,306 basepairs and by 32,332,274 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 202.0 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 202.0 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: June 15 2014, 202.0). 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
202.0, 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 202.0

1.3.1 Organizational changes

The total number of sequence data files increased by 43 with this release:

  - the BCT division is now composed of 136 133 files (+3)
  - the CON division is now composed of 267 246 files (+21)
  - the ENV division is now composed of  73 69 files (+4)
  - the EST division is now composed of 475 files (-1)
  - the GSS division is now composed of 287 285 files (+2)
  - the INV division is now composed of  39 files (+1)
  - the PAT division is now composed of 209 files (+5)
  - the PLN division is now composed of  70 68 files (+2)
  - the TSA division is now composed of 156 files (+6)

  Note that the loss of one EST data file is not due to removal of EST sequences.
Rather, we suspect that the combination of low EST data volumes since April,
combined with variability in gzip compression, simply happened to yield one
fewer file for this June release.

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 123
of the GSS flatfiles in Release 202.0. Consider gbgss165.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                            June 15 2014

                NCBI-GenBank Flat File Release 202.0

                           GSS Sequences (Part 1)

   87040 loci,    63874629 bases, from    87040 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "165" 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 _will_ be classes of GenBank sequences that
are not assigned GIs in the not-too-distant future. 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.

  And in fact, NCBI now has at least one WGS submission for which GIs have
not been assigned, for both the contigs and the scaffolds : ALWZ02.

Here are excerpts of the flatfile representation for the first ALWZ02 contig,
and the 'singleton' scaffold which is constructed from it:

LOCUS       ALWZ020000001            701 bp    DNA     linear   PLN 28-MAY-2013
DEFINITION  Picea glauca contig316_0, whole genome shotgun sequence.
ACCESSION   ALWZ020000001 ALWZ020000000
VERSION     ALWZ020000001.1
DBLINK      BioProject: PRJNA83435
....
ORIGIN      
        1 cgttgtgttg gggcacccaa ccttggtgag gccgtattaa aaagtctacc tccaagccaa
       61 aatttgttct tatccatcct ccaactcgtc tttttgccta gtgctcccct atgtggacgt
      121 tttcgttgtg gaggagtttt tcgtttgggc gcccatcttg cgaactcacc ttgcattgcg
      181 tttggtcgcc caacttgtga acgtgccttg gattgcgttg gggcgcccaa gttgcggacg
      241 tgcggacgtg cctttctttg ccgacatgcc ttgcgtttgc gttgcggacg tgcaatgggg
      301 cccccagctt gctgacgtgc cttgcgttgc gttggggtgc ccaacttgcc gacgtgcctt
      361 gcgttgcgtt ggggcaccca accttggtga ggccgtatta aaaagtctac ctccaagata
      421 aaatttgttc ttatccatcc tctagctctt cttttagcct agtgctccct tgtgtggaca
      481 ttttcgttgt ggatcatttt ttcgtttagg tgcccatctt gcagacaagc cttgcgttgc
      541 gtttgggcac ccatcttgcg gacgcgcctt tcattgcgtt ggggcgccca acgttggtga
      601 ggccgtatta aaaagtctac ctccaagaca aaatttgttc ttatccatcc tccatctcgt
      661 ctttttgcct agtgctccct tgtgtggacg ttttcgttgc g
//

LOCUS       ALWZ02S0000001           701 bp    DNA     linear   CON 14-JUN-2013
DEFINITION  Picea glauca scaffold316, whole genome shotgun sequence.
ACCESSION   ALWZ02S0000001 ALWZ000000000
VERSION     ALWZ02S0000001.1
DBLINK      BioProject: PRJNA83435
....
CONTIG      join(ALWZ020000001.1:1..701)
//


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

Sample URLs from which ALWZ02 data may be obtained include:

  http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ALWZ02#contigs
  http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ALWZ02#scaffolds

  http://www.ncbi.nlm.nih.gov/Traces/wgs/?download=ALWZ02.gbff.1.gz
  http://www.ncbi.nlm.nih.gov/Traces/wgs/?download=ALWZ02S.gbff.1.gz

  ftp://ftp.ncbi.nlm.nih.gov/genbank/wgs/wgs.ALWZ.1.gbff.gz
  ftp://ftp.ncbi.nlm.nih.gov/genbank/wgs/wgs.ALWZ.scflds.1.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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