Greetings GenBank Users,
GenBank Release 150.0 is now available via ftp from the National
Center for Biotechnology Information (NCBI):
Ftp Site Directory Contents
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ftp.ncbi.nih.gov genbank GenBank Release 150.0 flatfiles
ncbi-asn1 ASN.1 data used to create Release 150.0
Close-of-data was 10/08/2005. Five business days were required to build
Release 150.0. Uncompressed, the Release 150.0 flatfiles require
approximately
187 GB (sequence files only) or 205 GB (including the 'short directory' and
'index' files). The ASN.1 version requires approximately 164 GB. From
the release notes:
Release Date Base Pairs Entries
149 Aug 2005 51674486881 46947388
150 Oct 2005 53655236500 49152445
In the eight week period between the close dates for GenBank Releases 149.0
and 150.0, the non-WGS portion of GenBank grew by 1,980,749,619 basepairs
and by 2,205,057 sequence records. During that same period, 764,308 records
were updated. Combined, this yields an average of about 55,000 new and/or
updated records per day.
Between releases 149.0 and 150.0, the WGS component of GenBank grew by
2,816,201,863 basepairs and by 893,287 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 150.0 and Upcoming Changes) have been appended
below.
**NOTE** Problems were encountered generating the gbacc.idx and
gbkey.idx 'index' files that accompany GenBank Releases. See Section
1.3.1 for further details.
Release 150.0 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: October 15 2005, 150.0). 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 with 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
150.0, please send email outlining your difficulties to:
info at ncbi.nlm.nih.gov
Mark Cavanaugh, Vladimir Alekseyev, Aleksey Vysokolov, Michael Kimelman
GenBank
NCBI/NLM/NIH/HHS
1.3 Important Changes in Release 150.0
1.3.1 Problems generating accession number and keyword indexes
Continuing software problems again prevented the generation of
the gbacc.idx and gbkey.idx 'index' files which normally accompany
GenBank releases.
A version of gbacc.idx was built manually. However, the first field
contains just an accession number rather than Accession.Version .
The gbkey.idx index could not be created without substantial
additional delays in release processing, so it is completely absent
from 150.0 .
Our apologies for any inconvenience that this ongoing problem
may cause.
1.3.2 Organizational changes
The total number of sequence data files increased by 37 with this release:
- the BCT division is now comprised of 12 files (+1)
- the EST division is now comprised of 436 files (+23)
- the GSS division is now comprised of 158 files (+7)
- the HTC division is now comprised of 10 files (+3)
- the INV division is now comprised of 8 files (+1)
- the ROD division is now comprised of 21 files (+1)
- the VRT division is now comprised of 10 files (+1)
1.3.3 New qualifiers for the source feature
A set of five new source feature qualifiers are now legal as of this
October 2005 release.
Qualifier /lat_lon
Definition geographical coordinates of the location where
the specimen was collected
Value format "text"
Example /lat_lon="47.94 N 28.12 W"
Comment decimal degrees latitude [N/S] decimal degrees
longitude [E/W]
Qualifier /collected_by
Definition name of the person who collected the specimen
Value format "text"
Example /collected_by="Dan Janzen"
Qualifier /collection_date
Definition date that the specimen was collected
Value format "DD-MMM-YYYY", "MMM-YYYY" or "YYYY"
Example /collection_date="21-OCT-1952"
/collection_date="OCT-1952"
/collection_date="1952"
Comment full date format DD-MMM-YYYY is preferred;
where day and/or month of collection is not known either "MMM-YYYY"
or "YYYY"
can be used; three-letter month abbreviation can be one of the
following:
JAN, FEB, MAR, APR, MAY, JUN, JUL, AUG, SEP, OCT, NOV, DEC.
Qualifier /identified_by
Definition name of the taxonomist who identified the
specimen
Value format "text"
Example /identified_by="John Burns"
Qualifier /PCR_primers
Definition PCR primers that were used to amplify the
sequence.
Value format /PCR_primers="fwd_name:XXX, fwd_seq:xxxxx,
rev_name:YYY, rev_seq:yyyyy"
Example /PCR_primers="fwd_name:CO1P1,
fwd_seq:ttgattttttggtcayccwgaagt,
rev_name:CO1R4, rev_seq:ccwvytardcctarraartgttg"
Comment fwd_seq and rev_seq are both required.
fwd_name and rev_name are both optional.
Both sequences should be presented in 5'>3'
order.
The sequences should utilize the IUPAC
degenerate-base alphabet.
For the /PCR_primers qualifier, the order of the elements within the
qualifier value must always be as shown above. Multiple /PCR_primers
qualifiers may exist on a source feature.
These qualifiers will most likely see their first use in association
with environmental sampling projects and the BarCode project.
1.3.4 : /evidence qualifer replaced
Two new qualifiers which replace /evidence are legal as of the
October 2005 GenBank release :
/experiment
/inference
Existing /evidence="not_experimental" qualifiers have been replaced by:
/inference="non-experimental evidence, no additional details recorded"
While existing /evidence="experimental" qualifiers are now:
/experiment="experimental evidence, no additional details recorded"
The complete definitions of these two new qualifiers are as follows:
Qualifier /experiment
Definition a brief description of the nature of the
experimental
evidence that supports the feature
identification
or assignment.
Value format "text"
Example /experiment="Northern blot"
Comment detailed experimental details should not be
included,
and would normally be found in the cited
publications.
/experiment="experimental evidence, no
additional details recorded"
is for use purely to replace existing instances
of
/evidence=EXPERIMENTAL
Qualifier /inference
Definition a structured description of non-experimental
evidence
that supports the feature identification or
assignment.
Value format "TYPE[ (same species)][:EVIDENCE_BASIS]"
where TYPE is one of the following:
"non-experimental evidence, no additional
details recorded"
"similar to sequence"
"similar to AA sequence"
"similar to DNA sequence"
"similar to RNA sequence"
"similar to RNA sequence, mRNA"
"similar to RNA sequence, EST"
"similar to RNA sequence, other RNA"
"profile"
"nucleotide motif"
"protein motif"
"ab initio prediction"
where the optional text " (same species)" is included when the
inference
comes from the same species as the entry.
where the optional "EVIDENCE_BASIS" is either a reference to a
database
entry (including accession and version) or an algorithm (including
version),
eg 'INSD:AACN010222672.1', 'InterPro:IPR001900', 'ProDom:PD000600',
'Genscan:2.0', etc.
Example /inference="similar to DNA
sequence:INSD:AY411252.1"
/inference="similar to RNA, mRNA
sequence:RefSeq:NM_000041.2"
/inference="similar to DNA sequence (same
species):INSD:AACN010222672.1"
/inference="profile:tRNAscan:2.1"
/inference="protein motif:InterPro:IPR001900"
/inference="ab initio prediction:Genscan:2.0"
Comment /inference="non-experimental evidence, no
additional details recorded"
is for use purely to replace existing instances
of
/evidence=NOT_EXPERIMENTAL
1.3.5 New /organelle qualifier value
As of the October 2005 GenBank release, a new value for the /organelle
qualifier is now supported : hydrogenosome
This will be used for the annotation of sequences from anaerobic protozoa
and fungi, for which the hydrogenosome has a role in anaerobic respiration.
1.3.6 Two new qualifiers for trans splicing and ribosomal slippage
As of the October 2005 GenBank release, these two new qualifiers
have been introduced:
Qualifier /trans_splicing
Definition indicates that exons from two RNA molecules are
ligated in intermolecular reaction to form
mature RNA
Value format none
Example /trans_splicing
Comment should be used on features such as CDS, mRNA and
other features that are produced as a result of
a
trans-splicing event. This qualifier should be
used only
when the splice event is indicated via the join
operator
for the associated feature's location.
Note : legal on CDS, mRNA, misc_RNA, precursor_RNA, 5'UTR, 3'UTR,
tRNA,
and gene features
Qualifier /ribosomal_slippage
Definition during protein translation, certain sequences
can
program ribosomes to change to an alternative
reading frame by a mechanism known as ribosomal
slippage
Value format none
Example /ribosomal_slippage
Comment a join operator,e.g.:
[join(486..1784,1787..4810)]
should be used in the CDS spans to indicate the
location of ribosomal_slippage
Note: legal on CDS features only
1.3.7 New /exception qualifier value
Coding regions for which the conceptual protein translation differs from
the supplied /translation qualifier are flagged with an /exception
qualifier. The value :
"rearrangement required for product"
is now legal for /exception as of this October 2005 GenBank release.
1.3.8 : /repeat_unit qualifer replaced
Two new qualifiers designed to replace /repeat_unit are now legal as of
the October 2005 GenBank release : /repeat_unit_seq and /repeat_unit_range .
The old qualifier accomodates both integer ranges (eg: "10..20") and
characters that represent a repeat unit pattern (eg: (AT)2(AA)5 ).
Introducing
a separate qualifier for each of these representations will make it easier
to submit and validate their values.
Qualifier /rpt_unit_seq
Definition identity of a repeat sequence
Value format "text"
Example /rpt_unit_seq="aagggc"
/rpt_unit_seq="ag(5)tg(8)"
Comment used to indicate the literal sequence that
constitutes
a repeated sequence specified by the feature keys
oriT,
repeat_region, repeat_unit and satellite.
Note : legal on oriT, repeat_region, repeat_unit and satellite
features
Qualifier /rpt_unit_range
Definition identity of a repeat range
Value format "text"
Example /rpt_unit_range="202..245"
Comment used to indicate the base range of the sequence that
constitutes a repeated sequence specified by the
feature keys oriT, repeat_region, repeat_unit and
satellite.
Note : legal on oriT, repeat_region, repeat_unit and satellite
features
1.3.9 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 from 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
twenty-eight of the GSS flatfiles in Release 150.0. Consider gbgss131.seq :
GBGSS1.SEQ Genetic Sequence Data Bank
October 15 2005
NCBI-GenBank Flat File Release 150.0
GSS Sequences (Part 1)
87189 loci, 64730126 bases, from 87189 reported sequences
Here, the filename and part number in the header is "1", though the file
has been renamed as "131" based on the number of files dumped from the other
system. We will work to resolve this discrepancy in future releases, but
the
priority is certainly much lower than many other tasks.
1.4 Upcoming Changes
1.4.1 New Linetype for Genome Project Identifier
DDBJ, EMBL, and GenBank are working to create a collaborative system that
will assign a unique numeric identifier to genome projects. The purpose of
this new identifier is to provide a link among sequence records that pertain
to a specific genome sequencing project.
At GenBank, this new identifier will be presented in the flatfile format
via a new linetype : PROJECT . Here is a mocked-up example demonstrating
the new linetype's use:
LOCUS CH476840 1669278 bp DNA linear CON
05-OCT-2005
DEFINITION Magnaporthe grisea 70-15 supercont5.200 genomic scaffold, whole
genome shotgun sequence.
ACCESSION CH476840 AACU02000000
VERSION CH476840.1 GI:77022292
PROJECT GENOME_PROJECT:12345
The integer 12345 represents the value of a possible genome project
identifier.
There is a possibility that the contents of the PROJECT line might change
somewhat from this example by the time the new identifier is implemented.
We will keep you posted of any such changes via these release notes and the
GenBank listserv.
These Genome Project identifiers will be searchable within NCBI's
Entrez: Genome-Project database:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj
The earliest date on which this new linetype will appear in the GenBank
flatfile format is February 15 2006.
Hanzhen Sun for Mark Cavanaugh
Hanzhen Sun
------------
CONTRACTOR
NIH/NLM/NCBI
301-496-4956
