Greetings GenBank Users,
GenBank Release 209.0 is now available via FTP from the National Center
for Biotechnology Information (NCBI):
Ftp Site Directory Contents
---------------- --------- ---------------------------------------
ftp.ncbi.nih.gov genbank GenBank Release 209.0 flatfiles
ncbi-asn1 ASN.1 data used to create Release 209.0
Close-of-data for GenBank 209.0 occurred on 08/14/2015. Uncompressed,
the Release 209.0 flatfiles require roughly 735 GB (sequence files only).
The ASN.1 data require approximately 600 GB.
Recent statistics for 'traditional' sequences (including non-bulk-oriented
TSA, and excluding WGS and the CON-division):
Release Date Base Pairs Entries
208 Jun 2015 193921042946 185019352
209 Aug 2015 199823644287 187066846
Recent statistics for WGS sequencing projects:
Release Date Base Pairs Entries
208 Jun 2015 1038937210221 258702138
209 Aug 2015 1163275601001 302955543
Recent statistics for bulk-oriented TSA sequencing projects:
208 Jun 2015 60697472570 76974601
209 Aug 2015 69360654413 87827013
During the 57 days between the close dates for GenBank Releases 208.0
and 209.0, the 'traditional' portion of GenBank grew by 5,902,601,341
basepairs and by 2,047,494 sequence records. During that same period,
288,641 records were updated. An average of 40,985 'traditional' records
were added and/or updated per day.
Between releases 208.0 and 209.0, the WGS component of GenBank grew by
124,338,390,780 basepairs and by 44,253,405 sequence records.
Between releases 208.0 and 209.0, the TSA component of GenBank grew by
8,663,181,843 basepairs and by 10,852,412 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 209.0 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: Removal of NCBI GI sequence identifiers from GenBank, GenPept,
and FASTA sequence formats. Users who make use of GIs in their information
systems and analysis pipelines should take particular note of that section.
Release 209.0 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 2015, 209.0). 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
209.0, 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 209.0
1.3.1 Organizational changes
The total number of sequence data files increased by 59 with this release:
- the BCT division is now composed of 196 files (+9)
- the CON division is now composed of 323 files (+4)
- the ENV division is now composed of 85 files (+4)
- the GSS division is now composed of 299 files (+2)
- the INV division is now composed of 129 files (+1)
- the MAM division is now composed of 28 files (+19)
- the PAT division is now composed of 229 files (+6)
- the PHG division is now composed of 3 files (+1)
- the PLN division is now composed of 114 files (+2)
- the VRL division is now composed of 37 files (+1)
- the VRT division is now composed of 56 files (+10)
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 127
of the GSS flatfiles in Release 209.0. Consider gbgss173.seq :
GBGSS1.SEQ Genetic Sequence Data Bank
August 15 2015
NCBI-GenBank Flat File Release 209.0
GSS Sequences (Part 1)
87032 loci, 63853715 bases, from 87032 reported sequences
Here, the filename and part number in the header is "1", though the file
has been renamed as "173" 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 removed from GenBank/GenPept/FASTA formats
As of 06/15/2016, the integer sequence identifiers known as "GIs" will no
longer be included in the GenBank, GenPept, and FASTA formats supported by
NCBI for the display of sequence records.
As first described in the Release Notes for GenBank 199.0 in December 2013,
NCBI is in the process of moving to storage solutions which utilize only
Accession.Version identifiers. See Section 1.4.2 of these release notes for
additional background information about those developments.
Although GI sequence identifiers served their purpose well for many years,
the Accession.Version system is completely equivalent (and much more
human-readable).
And given the shift to non-GI-based systems, the importance of using
Accession.Version identifiers cannot be overstated. So as an initial step, NCBI
will cease the display of GI identifiers in the flatfile and FASTA views of
all sequence records.
Previously-assigned GI identifiers will continue to exist 'behind the scenes',
and NCBI services (including URLs, APIs, etc) which accept GIs as inputs/arguments
will be supported, for those sequence records that have GIs, for the foreseeable
future.
Over the next year NCBI will identify all such services that do not yet
support Accession.Version identifiers, and add that support. Users of those
services will then be encouraged to make use of Accession.Version rather than GIs.
Of course, for those services that already support Accession.Version, NCBI
encourages users to begin transitioning away from GI as soon as is practical.
In the sample record below, nucleotide sequence AF123456 has been assigned a
GI of 6633795, and the protein translation of its coding region feature has
been assigned a GI of 6633796 :
LOCUS AF123456 1510 bp mRNA linear VRT 12-APR-2012
DEFINITION Gallus gallus doublesex and mab-3 related transcription factor 1
(DMRT1) mRNA, partial cds.
ACCESSION AF123456
VERSION AF123456.2 GI:6633795
....
CDS <1..936
/gene="DMRT1"
/note="cDMRT1"
/codon_start=1
/product="doublesex and mab-3 related transcription factor
1"
/protein_id="AAF19666.1"
/db_xref="GI:6633796"
/translation="PAAGKKLPRLPKCARCRNHGYSSPLKGHKRFCMWRDCQCKKCSL
IAERQRVMAVQVALRRQQAQEEELGISHPVPLPSAPEPVVKKSSSSSSCLLQDSSSPA
HSTSTVAAAAASAPPEGRMLIQDIPSIPSRGHLESTSDLVVDSTYYSSFYQPSLYPYY
NNLYNYSQYQMAVATESSSSETGGTFVGSAMKNSLRSLPATYMSSQSGKQWQMKGMEN
RHAMSSQYRMCSYYPPTSYLGQGVGSPTCVTQILASEDTPSYSESKARVFSPPSSQDS
GLGCLSSSESTKGDLECEPHQEPGAFAVSPVLEGE"
After June 15 2016, the GI value on the VERSION line and the GI /db_xref
qualifier for the coding region feature will no longer be displayed:
LOCUS AF123456 1510 bp mRNA linear VRT 12-APR-2012
DEFINITION Gallus gallus doublesex and mab-3 related transcription factor 1
(DMRT1) mRNA, partial cds.
ACCESSION AF123456
VERSION AF123456.2
....
CDS <1..936
/gene="DMRT1"
/note="cDMRT1"
/codon_start=1
/product="doublesex and mab-3 related transcription factor
1"
/protein_id="AAF19666.1"
/translation="PAAGKKLPRLPKCARCRNHGYSSPLKGHKRFCMWRDCQCKKCSL
IAERQRVMAVQVALRRQQAQEEELGISHPVPLPSAPEPVVKKSSSSSSCLLQDSSSPA
HSTSTVAAAAASAPPEGRMLIQDIPSIPSRGHLESTSDLVVDSTYYSSFYQPSLYPYY
NNLYNYSQYQMAVATESSSSETGGTFVGSAMKNSLRSLPATYMSSQSGKQWQMKGMEN
RHAMSSQYRMCSYYPPTSYLGQGVGSPTCVTQILASEDTPSYSESKARVFSPPSSQDS
GLGCLSSSESTKGDLECEPHQEPGAFAVSPVLEGE"
Similarly, the GI value will be removed from the VERSION line of the GenPept
format. Currently:
LOCUS AAF19666 311 aa linear VRT 12-APR-2012
DEFINITION doublesex and mab-3 related transcription factor 1, partial [Gallus
gallus].
ACCESSION AAF19666
VERSION AAF19666.1 GI:6633796
DBSOURCE accession AF123456.2
....
CDS 1..311
/gene="DMRT1"
/coded_by="AF123456.2:<1..936"
As of 06/15/2016:
LOCUS AAF19666 311 aa linear VRT 12-APR-2012
DEFINITION doublesex and mab-3 related transcription factor 1, partial [Gallus
gallus].
ACCESSION AAF19666
VERSION AAF19666.1
DBSOURCE accession AF123456.2
....
CDS 1..311
/gene="DMRT1"
/coded_by="AF123456.2:<1..936"
Note that the coding region feature for GenPept format has never included
the display of nucleotide GI values.
For FASTA format, GI values will be removed from the FASTA header/defline:
Currently:
>gi|6633795|gb|AF123456.2| Gallus gallus doublesex and mab-3 related transcription factor 1 (DMRT1) mRNA, partial cds
CCGGCGGCGGGCAAGAAGCTGCCGCGTCTGCCCAAGTGTGCCCGCTGCCGCAACCACGGCTACTCCTCGC
CGCTGAAGGGGCACAAGCGGTTCTGCATGTGGCGGGACTGCCAGTGCAAGAAGTGCAGCCTGATCGCCGA
[....]
>gi|6633796|gb|AAF19666.1| doublesex and mab-3 related transcription factor 1, partial
[Gallus gallus]
PAAGKKLPRLPKCARCRNHGYSSPLKGHKRFCMWRDCQCKKCSLIAERQRVMAVQVALRRQQAQEEELGI
SHPVPLPSAPEPVVKKSSSSSSCLLQDSSSPAHSTSTVAAAAASAPPEGRMLIQDIPSIPSRGHLESTSD
LVVDSTYYSSFYQPSLYPYYNNLYNYSQYQMAVATESSSSETGGTFVGSAMKNSLRSLPATYMSSQSGKQ
WQMKGMENRHAMSSQYRMCSYYPPTSYLGQGVGSPTCVTQILASEDTPSYSESKARVFSPPSSQDSGLGC
LSSSESTKGDLECEPHQEPGAFAVSPVLEGE
As of 06/15/2016:
>gb|AF123456.2| Gallus gallus doublesex and mab-3 related transcription factor 1 (DMRT1) mRNA, partial cds
CCGGCGGCGGGCAAGAAGCTGCCGCGTCTGCCCAAGTGTGCCCGCTGCCGCAACCACGGCTACTCCTCGC
CGCTGAAGGGGCACAAGCGGTTCTGCATGTGGCGGGACTGCCAGTGCAAGAAGTGCAGCCTGATCGCCGA
[....]
>gb|AAF19666.1| doublesex and mab-3 related transcription factor 1, partial
[Gallus gallus]
PAAGKKLPRLPKCARCRNHGYSSPLKGHKRFCMWRDCQCKKCSLIAERQRVMAVQVALRRQQAQEEELGI
SHPVPLPSAPEPVVKKSSSSSSCLLQDSSSPAHSTSTVAAAAASAPPEGRMLIQDIPSIPSRGHLESTSD
LVVDSTYYSSFYQPSLYPYYNNLYNYSQYQMAVATESSSSETGGTFVGSAMKNSLRSLPATYMSSQSGKQ
WQMKGMENRHAMSSQYRMCSYYPPTSYLGQGVGSPTCVTQILASEDTPSYSESKARVFSPPSSQDSGLGC
LSSSESTKGDLECEPHQEPGAFAVSPVLEGE
Please direct any inquiries about these changes to the NCBI Service Desk:
info from ncbi.nlm.nih.gov
1.4.2 GI sequence identifiers are being phased out at NCBI
The numeric GI sequence identifier that NCBI used to assign 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 over 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 is
being implemented gradually. Unannotated WGS projects consisting of millions
of contigs and scaffolds, and unannotated TSA projects, are the first two
classes of records for which GIs are no longer being assigned. But the practice
will ultimately expand to include other classes of records.
If GIs are central to your operations, NCBI strongly urges that you begin
planning a switch to the use of Accession.Version identifiers instead.
The contigs and scaffolds of the ALWZ04 WGS project are good examples of
sequences that lack GIs. Below are excerpts from the flatfile representation
of the first ALWZ04 contig, and the 'singleton scaffold' which is constructed
from it. Note the absence of a GI value on the VERSION line of these two
records:
LOCUS ALWZ040000001 1191 bp DNA linear PLN 13-MAR-2015
DEFINITION Picea glauca, whole genome shotgun sequence.
ACCESSION ALWZ040000001 ALWZ040000000
VERSION ALWZ040000001.1
DBLINK BioProject: PRJNA83435
BioSample: SAMN01120252
....
ORIGIN
1 ctataatacc cctatgccaa acgaacccaa ttgtaaatgt aaatgcaaat gtacttaggc
61 tggttagttg tttaatatca ttttttgtat gcaccttcca tggtataatg cgcacatgta
121 tagcgcacta aaattatgaa gtgtgcccat tccaagatat tgcgcgtaaa aaacttaagt
181 gtgcatgatt ttgagactag ggagactttg tgtatatgtt gtgttttata tgctggagag
241 acaattatta ttagttagga ggattatgtt ttgtactagg caagagagcc tagatgttaa
301 aggctagtga gcctattttt gtatatgtct catcattaat ataatacatc attgtgtgta
....
901 ttgttgggaa ttgatttcct gaatgtgtta aactgcattg atagggatct gagaattcct
961 ttctggccta ttgctgaagc tttggaaggg aggtggggca accgagggac tgttgagaag
1021 agaagggtca cacttcctgg ggtgggacaa gcatgtgggg aattagggat tgcaggatgt
1081 tagtttgaat tggcacctat gacagagtct ttcctattgt ctgagatatg tcagcttggt
1141 taggaaaccc tttacctggg tagagtttag tcccagctcg ggggtgaccc a
//
LOCUS ALWZ04S0000001 1191 bp DNA linear CON 13-MAR-2015
DEFINITION Picea glauca Pg-01r141201s0000001, whole genome shotgun sequence.
ACCESSION ALWZ04S0000001 ALWZ0400000000
VERSION ALWZ04S0000001.1
DBLINK BioProject: PRJNA83435
BioSample: SAMN01120252
....
CONTIG join(ALWZ040000001.1:1..1191)
//
Sample URLs from which ALWZ04 data may be obtained include:
http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ALWZ04#contigshttp://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ALWZ04#scaffoldshttp://www.ncbi.nlm.nih.gov/Traces/wgs/?download=ALWZ04.gbff.1.gzhttp://www.ncbi.nlm.nih.gov/Traces/wgs/?download=ALWZ04S.gbff.1.gzftp://ftp.ncbi.nlm.nih.gov/genbank/wgs/wgs.ALWZ.*.gbff.gzftp://ftp.ncbi.nlm.nih.gov/genbank/wgs/wgs.ALWZ.scflds.*.gbff.gz
