[Genbank-bb] GenBank Release 150.0 is now available

Sun, Hanzhen (NIH/NLM/NCBI) hanzhen at ncbi.nlm.nih.gov
Fri Oct 14 15:17:50 EST 2005


Greetings GenBank Users,

  GenBank Release 150.0 is now available via ftp from the National
Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 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 



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