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[Genbank-bb] GenBank Release 200.0 Available : February 14 2014

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Fri Feb 14 16:57:50 EST 2014

Greetings GenBank Users,

  GenBank Release 200.0 (aka, "the SnowBank Release") is now available
via FTP from the National Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 200.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 200.0

  Close-of-data for GenBank 200.0 occurred on 02/12/2014. Uncompressed,
the Release 200.0 flatfiles require roughly 625 GB (sequence files only).
The ASN.1 data require approximately 522 GB.

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

  Release  Date      Base Pairs    Entries

  199      Dec 2013  156230531562  169331407
  200      Feb 2014  157943793171  171123749

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  199    Dec 2013  556764321498  133818570
  200    Feb 2014  591378698544  139725795

  During the 64 days between the close dates for GenBank Releases 199.0
and 200.0, the non-WGS/non-CON portion of GenBank grew by 1,713,261,609
basepairs and by 1,792,342 sequence records. During that same period,
4,979,722 records were updated. An average of 105,813 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 199.0 and 200.0, the WGS component of GenBank grew by
34,614,377,046 basepairs and by 5,907,225 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 200.0 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 200.0 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 2014, 200.0). 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
200.0, 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 200.0

1.3.1 Organizational changes

The total number of sequence data files increased by 34 with this release:

  - the BCT division is now composed of 118 files (+4)
  - the CON division is now composed of 242 files (+11)
  - the GSS division is now composed of 284 files (+5)
  - the INV division is now composed of  38 files (+2)
  - the PAT division is now composed of 204 files (+5)
  - the PLN division is now composed of  67 files (+2)
  - the PRI division is now composed of  47 files (+1)
  - the TSA division is now composed of 150 files (+3)
  - the VRT division is now composed of  32 files (+1)

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 121
of the GSS flatfiles in Release 200.0. Consider gbgss164.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                        February 15 2014

                NCBI-GenBank Flat File Release 200.0

                           GSS Sequences (Part 1)

   87039 loci,    63873952 bases, from    87039 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "164" 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:


 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
        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:




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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