GenBank Release 174.0 Now Available

[Cavanaugh, Mark (NIH/NLM/NCBI) [E]]

Greetings GenBank Users,

  GenBank Release 174.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 174.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 174.0

  Close-of-data for GenBank 174.0 occurred on 10/16/2009. Uncompressed,
the Release 174.0 flatfiles require roughly 416 GB (sequence files only)
or 445 GB (including the 'short directory', 'index' and the *.txt
files). The ASN.1 data require approximately 376 GB.

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

  Release  Date      Base Pairs    Entries

  173      Aug 2009  106533156756  108431692
  174      Oct 2009  108560236506  110946879

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  173      Aug 2009  148165117763  48443067
  174      Oct 2009  149348923035  48119301

  During the 56 days between the close dates for GenBank Releases 173.0
and 174.0, the non-WGS/non-CON portion of GenBank grew by 2,027,079,750
basepairs and by 2,515,187 sequence records. During that same period,
467,858 records were updated. An average of about 53,269 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 173.0 and 174.0, the WGS component of GenBank grew by
1,183,805,272 basepairs, while the number of sequence records decreased
by 323,766 (due to the re-assembly of some WGS projects into fewer, but
larger, 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 174.0 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 1.3.4 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 174.0 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: August 15 2009, 174.0). 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
174.0, please send email outlining your difficulties to:

        info@...

Mark Cavanaugh, Michael Kimelman, Ilya Dondoshansky, Sergey Zhdanov
GenBank
NCBI/NLM/NIH/HHS

1.3 Important Changes in Release 174.0

1.3.1 Organizational changes

The total number of sequence data files increased by 31 with this
release:

  - the CON division is now composed of 132 files (+1)
  - the ENV division is now composed of  22 files (+5)
  - the EST division is now composed of 892 files (+6)
  - the GSS division is now composed of 350 files (+10)
  - the INV division is now composed of  19 files (+1)
  - the PAT division is now composed of  85 files (+6)
  - the VRL division is now composed of  13 files (+1)
  - the VRT division is now composed of  20 files (+1)

The total number of 'index' files increased by 3 with this release:

  - the AUT (author) index is now composed of 69 files (+3)

1.3.2 New class of /exception value

  As of this October 2009 release, a new class of /exception is
available
for use on coding region features:

   /exception="annotated by transcript or proteomic data"

  This exception can be used if: a) the protein sequence (presented via
a
coding region's /translation qualifier) differs from the conceptual
translation; b) the quality of the DNA sequencing is high; and c) there
is evidence at the transcript or proteome level that the presented
protein
*is* actually expressed by the organism.

  An inference qualifier of type "similar to" should be used in
conjunction
with this new type of exception, to indicate the supporting
EST/cDNA/protein
sequence.

  An update to the definition of the /exception qualifier which
incorporates
the new class will be provided via the GenBank newsgroup within a few
weeks.

1.3.3 /haplogroup qualifier introduced

  A haplotype is a combination of alleles at multiple loci that are
transmitted together on the same chromosome. A haplogroup is a group of
similar haplotypes that share a common ancestor with a single nucleotide
polymorphism mutation. The majority of submitters of complete human
mitochondrial genomes provide information about their haplogroup rather
than
their haplotype. Stable mtDNA polymorphic variants clustered together in
specific combination form a haplogroup.

  To accommodate this need, a new /haplogroup qualifier has been
introduced
as of this October 2009 GenBank Release.

  A formal definition of /haplogroup will be provided via the GenBank
newsgroup within a few weeks.
 
1.3.4 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@...

  Our apologies for any inconvenience that these changes may cause.

1.3.5 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
seventy-eight of the GSS flatfiles in Release 174.0. Consider
gbgss273.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                         October 15 2009

                NCBI-GenBank Flat File Release 174.0

                           GSS Sequences (Part 1)

   87177 loci,    64203737 bases, from    87177 reported sequences

  Here, the filename and part number in the header is "1", though the
file
has been renamed as "273" 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 /artificial_location qualifier introduced

  A new qualifier, intended for use in limited genome-scale annotation
contexts, will be introduced as of GenBank Release 175.0 in December
2009:

Qualifier /artificial_location

Definition indicates that location of the CDS or mRNA is modified
to
                adjust for the presence of a frameshift or internal stop
                codon and not because of biological processing between
the
                regions.  This is expected to be used only for
genome-scale
                annotation, either because a heterogeneous population
was
                sequenced, or because the feature is in a region of
                low-quality sequence.

1.4.2 New /pseudogene and /non_functional qualifiers

  The GenBank 173.0 release notes described an anticipated conversion
of the /pseudo qualifier to /non_functional, based on the results of
the May 2009 INSDC annual meeting:

    "Because the term "pseudo" is often assumed to mean 'pseudogene',
     the /pseudo qualifier will be renamed as /non_functional, to
     better reflect its actual usage in the sequence databases."

  During follow-up discussions, the INSDC members decided that existing
uses of /pseudo can include both of the possible meanings of the term,
and that a more conservative course would be to introduce two new
qualifiers:

    /pseudogene
    /non_functional

  Sequence submission tools will be updated to utilize these, and
the ambiguous /pseudo qualifier will be deprecated. If it is
possible, existing instances of /pseudo would then be converted
to one of the two new qualifiers.

  /pseudogene and /non_functional will become legal for the Feature
Table as of the April 2010 GenBank Release.


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