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[Genbank-bb] GenBank Release 204.0 Available : October 20 2014

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Mon Oct 20 22:17:09 EST 2014

Greetings GenBank Users,

  GenBank Release 204.0 is now available via FTP from the National Center
for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 204.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 204.0

  Close-of-data for GenBank 204.0 occurred on 10/18/2014. Uncompressed,
the Release 204.0 flatfiles require roughly 680 GB (sequence files only).
The ASN.1 data require approximately 557 GB.

Recent statistics for non-WGS, non-CON sequences:

  Release  Date      Base Pairs    Entries

  203      Aug 2014  165722980375  174108750
  204      Oct 2014  181563676918  178322253

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  203    Aug 2014  774052098731  189080419
  204    Oct 2014  805549167708  196049974

  During the 63 days between the close dates for GenBank Releases 203.0
and 204.0, the non-WGS/non-CON portion of GenBank grew by 15,840,696,543
basepairs and by 4,213,503 sequence records. During that same period,
532,480 records were updated. An average of 75,333 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 203.0 and 204.0, the WGS component of GenBank grew by
31,497,068,977 basepairs and by 6,969,555 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 204.0 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 204.0 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 2014, 204.0). 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

Or, if the files are compressed, perhaps:

        gzcat $i | head -10 | grep Release

  If you encounter problems while ftp'ing or uncompressing Release
204.0, please send email outlining your difficulties to:

        info from ncbi.nlm.nih.gov

Mark Cavanaugh, Michael Kimelman, Ilya Dondoshansky, Sergey Zhdanov,

1.3 Important Changes in Release 204.0

1.3.1 Organizational changes

The total number of sequence data files increased by 123 with this release:

  - the BCT division is now composed of 152 142 files (+10)
  - the CON division is now composed of 286 278 files (+8)
  - the ENV division is now composed of  76  74 files (+2)
  - the EST division is now composed of 477 476 files (+1)
  - the INV division is now composed of 124  40 files (+84)
  - the PAT division is now composed of 214 210 files (+4)
  - the PLN division is now composed of  89  86 files (+3)
  - the VRT division is now composed of  44  33 files (+11)

  There is an unusually large increase in the number of INV-division sequence
files for Release 204. Nearly 3 million sequence records, with nearly
12 gigabases, which should have been handled as WGS projects, were distributed
by the European Nucleotide Archive (ENA) on September 22 2014 as individual
records. ENA has investigated the possibility of switching to a WGS
representation, but for the moment has decided that it isn't practical.
Hence, the unusual growth in the INV-division for this release.

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 123
of the GSS flatfiles in Release 204.0. Consider gbgss165.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                         October 15 2014

                NCBI-GenBank Flat File Release 204.0

                           GSS Sequences (Part 1)

   87046 loci,    63874704 bases, from    87046 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "165" 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 'Regulatory' feature to replace eleven existing feature types.

  As of the December 2015 GenBank release, eleven different features that
describe various aspects of regulation will be brought under the umbrella
of a single new feature: Regulatory . This new feature will have a
mandatory qualifier (/regulatory_class) to indicate the nature of its
regulatory activity.

  The existing features that will be replaced include: enhancer, promoter,
CAAT_signal, TATA_signal, -35_signal, -10_signal, RBS, GC_signal,
polyA_signal, attenuator, and terminator .

  A preliminary description of the new feature and qualifier is available,
and the October 2014 version of the Feature Table document will be updated
accordingly :

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Feature Key:	Regulatory

Definition:	any region of sequence that functions in the regulation of
		transcription or translation

Mandatory qualifiers:	/regulatory_class= "TYPE"

Optional qualifiers:	/allele="text"
			/inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]"
			/locus_tag="text" (single token)
			/old_locus_tag="text" (single token)

Comment:		This feature will replace the following Feature Keys
			in DEC-2014: enhancer, promoter, CAAT_signal,
			TATA_signal, -35_signal, -10_signal, RBS, GC_signal,
			polyA_signal, attenuator, terminator

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Qualifier:		/regulatory_class

Definition:		a structured description of the classification of
			transcriptional	and translational regulatory elements
			in a sequence                

Value format:		"TYPE"

Example:		/regulatory_class="promoter"

Comment:		TYPE is a term taken from the INSDC controlled
			vocabulary for regulatory classes; on 15-DEC-2014,
			the following terms were valid:

			"attenuator"  (replaces attenuator feature key)
			"CAAT_signal"  (replaces CAAT_signal Feature Key)
			"enhancer"  (replaces enhancer Feature Key)
			"GC_signal"  (replaces GC_signal Feature Key)
			"minus_35_signal" (replaces -10_signal Feature Key)
			"minus_10_signal"  (replaces -10_signal Feature Key)
			"polyA_signal_sequence"  (replaces polyA_signal Feature Key)
			"promoter" (replaces promoter Feature Key)
			"ribosome_binding_site" (replaces RBS feature key)
			"TATA_box"  (replaces TATA_signal Feature Key)
			"terminator" (replaces terminator feature key)

Comment:		regulatory classes not yet in the INSDC
			/regulatory_class controlled vocabulary can be
			annotated by entering /regulatory_class="other"
			together with :
			/note="[brief explanation of novel regulatory_class]"

1.4.2 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:


 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 several WGS submissions for which GIs have
not been assigned, for both the contigs and the scaffolds.

  For example: Here are excerpts of the flatfile representation for the
first ALWZ02 (second assembly-version of the ALWZ project) 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
        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:




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.

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