Greetings GenBank Users,
GenBank Release 201.0 is now available via FTP from the National Center
for Biotechnology Information (NCBI):
Ftp Site Directory Contents
---------------- --------- ---------------------------------------
ftp.ncbi.nih.gov genbank GenBank Release 201.0 flatfiles
ncbi-asn1 ASN.1 data used to create Release 201.0
Close-of-data for GenBank 201.0 occurred on 04/13/2014. Uncompressed,
the Release 201.0 flatfiles require roughly 625 GB (sequence files only).
The ASN.1 data require approximately 527 GB.
Recent statistics for non-WGS, non-CON sequences:
Release Date Base Pairs Entries
200 Feb 2014 157943793171 171123749
201 Apr 2014 159813411760 171744486
Recent statistics for WGS sequences:
Release Date Base Pairs Entries
200 Feb 2014 591378698544 139725795
201 Apr 2014 621015432437 143446790
During the 60 days between the close dates for GenBank Releases 200.0
and 201.0, the non-WGS/non-CON portion of GenBank grew by 1,869,618,589
basepairs and by 620,737 sequence records. During that same period,
2,046,345 records were updated. An average of 44,451 non-WGS/non-CON
records were added and/or updated per day.
Between releases 200.0 and 201.0, the WGS component of GenBank grew by
29,636,733,893 basepairs and by 3,720,995 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 201.0 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 201.0 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: April 15 2014, 201.0). 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
201.0, 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 201.0
1.3.1 Organizational changes
The total number of sequence data files increased by 27 with this release:
- the BCT division is now composed of 133 files (+15)
- the CON division is now composed of 246 files (+4)
- the ENV division is now composed of 69 files (+2)
- the EST division is now composed of 476 files (+1)
- the GSS division is now composed of 285 files (+1)
- the MAM division is now composed of 9 files (+1)
- the PLN division is now composed of 68 files (+1)
- the VRL division is now composed of 31 files (+2)
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 122
of the GSS flatfiles in Release 201.0. Consider gbgss164.seq :
GBGSS1.SEQ Genetic Sequence Data Bank
April 15 2014
NCBI-GenBank Flat File Release 201.0
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 "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:
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#contigshttp://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ALWZ02#scaffoldshttp://www.ncbi.nlm.nih.gov/Traces/wgs/?download=ALWZ02.gbff.1.gzhttp://www.ncbi.nlm.nih.gov/Traces/wgs/?download=ALWZ02S.gbff.1.gzftp://ftp.ncbi.nlm.nih.gov/genbank/wgs/wgs.ALWZ.1.gbff.gzftp://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.
