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[Genbank-bb] GenBank Release 188.0 Available : February 15 2012

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Wed Feb 15 17:45:08 EST 2012


Greetings GenBank Users,

  GenBank Release 188.0 is now available via FTP from the
National Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 188.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 188.0

  Close-of-data for GenBank 188.0 occurred on 02/11/2012. Uncompressed,
the Release 188.0 flatfiles require roughly 539 GB (sequence files only)
or 580 GB (including the 'short directory', 'index' and the *.txt files).
The ASN.1 data require approximately 442 GB.

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

  Release  Date      Base Pairs    Entries

  187      Dec 2011  135117731375  146413798
  188      Feb 2012  137384889783  149819246

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  187    Dec 2011  239868309609   73729553
  188    Feb 2012  261370512675   78656704

  During the 58 days between the close dates for GenBank Releases 187.0
and 188.0, the non-WGS/non-CON portion of GenBank grew by 2,267,158,408
basepairs and by 3,405,448 sequence records. During that same period,
428,497 records were updated. An average of 66,102 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 187.0 and 188.0, the WGS component of GenBank grew by
21,502,203,066 basepairs and by 4,927,151 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 188.0 and Upcoming Changes) have been appended
below for your convenience.

                ** Important Notes **

*  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 188.0 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 2012, 188.0). 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
188.0, 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 188.0

1.3.1 Organizational changes

The total number of sequence data files increased by 33 with this release:

  - the BCT division is now composed of  82 files (+2)
  - the CON division is now composed of 166 files (+4)
  - the ENV division is now composed of  50 files (+4)
  - the EST division is now composed of 455 files (+4)
  - the GSS division is now composed of 255 files (+4)
  - the HTC division is now composed of  15 files (+1)
  - the PAT division is now composed of 176 files (+3)
  - the PLN division is now composed of  53 files (+1)
  - the TSA division is now composed of  60 files (+9)
  - the VRL division is now composed of  20 files (+1)

The total number of 'index' files increased by 4 with this release:

  - the AUT (author name)  index is now composed of 96 files (+4)

1.3.2 Project DBLINKs transitioning to BioProject

  The Genome Project Database resource at the NCBI was redesigned in
recent months, culminating in the implementation of a new BioProject
resource:

        http://www.ncbi.nlm.nih.gov/bioproject

An article that describes the goals of BioProject is available:

        http://www.ncbi.nlm.nih.gov/books/NBK54015/

BioProject is a collaborative effort of the International Nucleotide
Sequence Database Collaboration (INSDC), and project data are exchanged 
with NCBI's partner INSDC institutions, EBI and DDBJ. A BioProject
website is also available at DDBJ:

        http://trace.ddbj.nig.ac.jp/bioproject/index_e.shtml

BioProjects are uniquely identified by BioProject Accession Numbers,
which utilize this format:

        "PRJ"
        "E" or "N" or "D"
        one letter
        one or more digits

Examples of valid BioProject accessions are PRJNA12521 and PRJEB1 .

With BioProject now in operation, we are preparing to implement links
from sequence records to the new resource. Previously, links to the
Genome Project Database were provided by numeric 'Project' DBLINKs .
Here's an example for a bacterial complete-genome record:

LOCUS       CP002497             1110245 bp    DNA     linear   PLN 14-NOV-2011
DEFINITION  Eremothecium cymbalariae DBVPG#7215 chromosome 1, complete
            sequence.
ACCESSION   CP002497
VERSION     CP002497.1  GI:356887709
DBLINK      Project: 60715

When this link is switched to a BioProject accession, the DBLINK
line will change slightly:

LOCUS       CP002497             1110245 bp    DNA     linear   PLN 14-NOV-2011
DEFINITION  Eremothecium cymbalariae DBVPG#7215 chromosome 1, complete
            sequence.
ACCESSION   CP002497
VERSION     CP002497.1  GI:356887709
DBLINK      BioProject: PRJNA60715

In the coming months, many millions of sequence records will gradually
be modified, to make use of the new BioProject DBLINK. They will not be
distributed via daily GenBank and RefSeq incremetal update products.
However, these new BioProject links *will* start to be seen in GenBank
and RefSeq release products as of December 2011. In addition, the new
BioProject links will become visible via NCBI's Entrez:Nucleotide
resource, as soon as the modification process begins. 

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 from January 2005
seemed 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
103 of the GSS flatfiles in Release 188.0. Consider gbgss153.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                        February 15 2012

                NCBI-GenBank Flat File Release 188.0

                           GSS Sequences (Part 1)

   87119 loci,    64001690 bases, from    87119 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "153" 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 New representation for Transcriptome Shotgun Assembly (TSA) records.

  The TSA division of GenBank has grown much more quickly than expected.
In order to accommodate the increasing TSA submission volume, GenBank plans 
to use a WGS-like approach for TSA projects.

  TSA projects will be assigned a four-letter project code, starting with
the letter "G" (for example, GAAA). Individual mRNA sequences within a 
project will make use of the 4+2+6 accession number convention, familiar
to users of WGS data (for example, GAAA01000001). Unlike WGS, there is
no concept of "re-assembly" for a TSA project, and so we expect that the
2-digit assembly-version number will always be "01" for TSA mRNAs. Similar
to WGS, a TSA master record will provide a convenient overview of a
TSA project, with an 'all-zeroes' accession number (eg: GAAA00000000) . 

  TSA projects that make use of this new representation will be provided
in a separate FTP directory at the NCBI FTP site: genbank/tsa . And like
WGS, the various data files for a TSA project will be grouped by the
4-letter project code, and they will be updated independently of the
GenBank release cycle.

  Plans aren't yet finalized for the 5.2 million TSA records currently
provided by the divisional gbtsa* files of a GenBank release. Ideally,
all would be converted to the new WGS-like representation, so that all 
TSA records in GenBank utilize a common approach. However, the resources
for such a conversion might not be readily available, in which case
older/legacy TSA records might remain as they are now.

  Further details about this new approach for handling TSA data will be
made available via these release notes and the GenBank newsgroup, as we
get closer to implementation. 

1.4.2 New /pseudogene qualifier; /pseudo will be deprecated

  A new controlled-vocabulary /pseudogene qualifier has been under
discussion within the INSDC since the last collaborative INSD meeting
in May 2011. The goal of the new qualifier is to use it for the annotation
of certain well-defined classes of pseudogenes. And at the same time,
to cease using the poorly-defined /pseudo qualifier, which has been
used for a variety of different situations by each INSDC member.

  Although a formal definition of /pseudogene is not yet available, we
do have a tentative list of the values for the new qualifier:

"processed" - the pseudogene has arisen by reverse
transcription of a mRNA into cDNA, followed by reintegration into the
genome. Therefore, it has lost any intron/exon structure, and it will
have a pseudo-polyA-tail (if a young pseudogene).

"unprocessed" - the pseudogene has arisen from a copy of
the parent gene by means other than reverse transcription. This covers
usually duplication (transposition [not retrotransposition] and perhaps
recombination) followed by accumulation of random mutation. The changes,
compared to their functional homolog, include insertion, deletions,
premature stop codons, frameshifts and a higher proportion of
non-synonymous versus synonymous substitutions.

"unitary" - the pseudogene has no parent. It is the
original gene, which is functional is some species but disrupted in some
way (indels, mutation, recombination) in another species or strain. In a
lot of cases, such changes would kill the organism, particularly with
house-keeping genes.

"allelic" - a (unitary) pseudogene that is stable in the
population but importantly it has a functional alternative allele also
in the population. i.e., one strain may have the gene, another strain
may have the pseudogene. MHC haplotypes have allelic pseudogenes.

"unknown" - would imply that the submitter does not know
the method of pseudogenisation

  If a final definition of /pseudogene can be arrived at within the
next few weeks, then the new qualifier would be legal as of GenBank
Release 190.0 in June of 2012. We will keep users posted about this
new qualifier via the GenBank newsgroup and these release notes.

1.4.3 Extension of position syntax for /anticodon qualifiers

  Starting with the April 2012 GenBank Release 189.0, the format
of the /anticodon qualifier will be extended to allow the use
of join() and complement() for the location of a tRNA's anticodon.

  Currently, the qualifier supports only a simple continuous
basepair range. For example:

	 /anticodon=(pos:34..36,aa:Phe)

  But there are rare cases of intron-containing tRNAs, for which a
simple X..Y location will not suffice:

     tRNA            join(<1..5,495..544)
                     /gene="trnL"
                     /product="tRNA-Leu"
                     /note="codon recognized: UUA"
                     /anticodon=(pos:join(5,495..496),aa:Leu)

  To support cases like these, the "pos" field will be allowed to
make use of the join() and complement() location operators.
Anticodons are usually three (sometimes four) bases in length, and 
this *remains* true even though the join() operator could theoretically
be (mis)used to assert a much more complex/larger location than that.





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