Greetings GenBank Users,
GenBank Release 173.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):
Ftp Site Directory Contents
---------------- --------- ---------------------------------------
ftp.ncbi.nih.gov genbank GenBank Release 173.0 flatfiles
ncbi-asn1 ASN.1 data used to create Release 173.0
Close-of-data for GenBank 173.0 occured on 08/21/2009. Uncompressed,
the Release 173.0 flatfiles require roughly 408 GB (sequence files only)
or 437 GB (including the 'short directory', 'index' and the *.txt
files). The ASN.1 data require approximately 370 GB.
Recent statistics for non-WGS, non-CON sequences:
Release Date Base Pairs Entries
172 Jun 2009 105277306080 106073709
173 Aug 2009 106533156756 108431692
Recent statistics for WGS sequences:
Release Date Base Pairs Entries
172 Jun 2009 145959997864 49063546
173 Aug 2009 148165117763 48443067
During the 72 days between the close dates for GenBank Releases 172.0
and 173.0, the non-WGS/non-CON portion of GenBank grew by 1,255,850,676
basepairs and by 2,357,983 sequence records. During that same period,
654,396 records were updated. An average of about 41,838
non-WGS/non-CON records were added and/or updated per day.
Between releases 172.0 and 173.0, the WGS component of GenBank grew
by 2,205,119,899 basepairs, while the number of sequence records decreased
by 620,479 (due to some WGS projects being re-assembled 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 173.0 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 1.3.5 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 173.0 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, 173.0). 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
173.0, 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 173.0
1.3.1 Organizational changes
The total number of sequence data files increased by 28 with this release:
- the BCT division is now composed of 48 files (+3)
- the ENV division is now composed of 17 files (+1)
- the EST division is now composed of 886 files (+11)
- the GSS division is now composed of 340 files (+3)
- the HTC division is now composed of 15 files (+1)
- the HTG division is now composed of 134 files (+1)
- the PAT division is now composed of 79 files (+6)
- the PLN division is now composed of 38 files (-1)
- the PRI division is now composed of 40 files (+1)
- the TSA division is now composed of 2 files (+1)
- the VRT division is now composed of 19 files (+1)
Note: The decline in the number of PLN division files is due to the fact that
twelve records representing the chromosomes of Oryza sativa Japonica Group
have been converted to a CON-division representation. See section 1.3.2 for
more details.
The total number of 'index' files increased by 1 with this release:
- the AUT (author) index is now composed of 66 files (+1)
1.3.2 Twelve Oryza sativa Japonica Group records moved to CON division.
Prior to Release 173.0, the sequence records for 12 Oryza sativa Japonica
Group chromosomes had been 'traditional' records, totalling over 382 Mbp of
sequence data.
However, on August 7 2009, the records were converted to a CON-division
representation, with CONTIG-line join() statements that describe how the
chromosomes are constructed from underlying PAC and fosmid sequences. The
records involved are:
LOCUS AP008207 45064769 bp DNA linear CON 07-AUG-2009
LOCUS AP008208 36823111 bp DNA linear CON 07-AUG-2009
LOCUS AP008209 37257345 bp DNA linear CON 07-AUG-2009
LOCUS AP008210 35863200 bp DNA linear CON 07-AUG-2009
LOCUS AP008211 30039014 bp DNA linear CON 07-AUG-2009
LOCUS AP008212 32124789 bp DNA linear CON 07-AUG-2009
LOCUS AP008213 30357780 bp DNA linear CON 07-AUG-2009
LOCUS AP008214 28530027 bp DNA linear CON 07-AUG-2009
LOCUS AP008215 23843360 bp DNA linear CON 07-AUG-2009
LOCUS AP008216 23661561 bp DNA linear CON 07-AUG-2009
LOCUS AP008217 30828668 bp DNA linear CON 07-AUG-2009
LOCUS AP008218 27757321 bp DNA linear CON 07-AUG-2009
Due to this change, these chromosomal records are now present in file
gbcon1.seq of the CON division. In addition, the total number of Oryza sativa
Japonica Group basepairs listed in the table in Section 2.2.7 has declined
by 370,461,808 bases, compared to Release 172.0. The table intentionally
excludes CON-division records, to avoid double-counting of underlying sequence
records and any larger-scale objects that are constructed from them.
1.3.3 File header problem for EST and GSS files
A new method of generating the EST and GSS sequence files has been
developed, which has reduced the time required to generate a GenBank
release by one day. However, a minor problem in the formatting of the
header of the sequence files was inadvertently introduced : a leading
space exists before the filename on the very first line. For example:
GBGSS100.SEQ Genetic Sequence Data Bank
August 15 2009
It should be:
GBGSS100.SEQ Genetic Sequence Data Bank
August 15 2009
The problem effects all EST files and most GSS files. We had hoped to
repair this formatting issue for Release 173.0, but the code changes
which were expected to fix the problem did not perform correctly. It
is hoped that this issue will be resolved for Release 174.0 .
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 from ncbi.nlm.nih.gov
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-two of the GSS flatfiles in Release 173.0. Consider gbgss269.seq :
GBGSS1.SEQ Genetic Sequence Data Bank
August 15 2009
NCBI-GenBank Flat File Release 173.0
GSS Sequences (Part 1)
87186 loci, 64231458 bases, from 87186 reported sequences
Here, the filename and part number in the header is "1", though the file
has been renamed as "269" 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 class of /exception value
As of October 2009, a new class of /exception will be available for use
on coding region features:
/exception="annotated by transcript or proteomic data"
This exception will be used for situations in which: the protein sequence
(presented via the coding region's /translation qualifier) differs from the
conceptual translation; the quality of the DNA sequencing is high; and 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 updated definition of /exception, with examples for this new type
of exception value, will be provided via the GenBank newsgroup prior to
the October release.
1.4.2 /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 accomodate this need, a new /haplogroup qualifier will be introduced as
of GenBank Release 174.0 in October 2009.
A formal definition of /haplogroup was not available as of the creation
of these release notes, so it will be provided via the GenBank newsgroup
prior to the October release.
1.4.3 /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.
1.4.4 /pseudo qualifier renamed as /non_functional
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. This change will take place
as of the April 2010 GenBank Release.
