Greetings GenBank Users,
GenBank Release 157.0 is now available via FTP from the National
Center for Biotechnology Information (NCBI):
Ftp Site Directory Contents
---------------- --------- ---------------------------------------
ftp.ncbi.nih.gov genbank GenBank Release 157.0 flatfiles
ncbi-asn1 ASN.1 data used to create Release 157.0
Close-of-data for GenBank 157.0 occured on 12/18/2006. Uncompressed, the
Release 157.0 flatfiles require roughly 243 GB (sequence files only)
or 254 GB (including the 'short directory', 'index' and the *.txt files).
The ASN.1 data require approximately 210 GB.
Recent statistics for non-WGS sequences:
Release Date Base Pairs Entries
156 Oct 2006 66925938907 62765195
157 Dec 2006 69019290705 64893747
And for WGS sequences:
Release Date Base Pairs Entries
156 Oct 2006 81127502509 18500772
157 Dec 2006 81611376856 18540918
During the 67 days between the close dates for GenBank Releases 156.0
and 157.0, the non-WGS portion of GenBank grew by 2,093,351,798 basepairs
and by 2,128,552 sequence records. During that same period, 840,919 records
were updated. An average of about 44,300 non-WGS records were added and/or
updated per day.
Between releases 156.0 and 157.0, the WGS component of GenBank grew by
483,874,347 basepairs and by 40146 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 157.0 and Upcoming Changes) have been appended
below.
** Important Note **
GenBank 'index' files are now provided without any EST content, and without
most GSS content. See Section 1.3.3 of the release notes for further details.
NCBI is considering ceasing support for the index files, so we strongly
encourage affected users to review that section and provide feedback.
Release 157.0 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: December 15 2006, 157.0). 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
157.0, 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 157.0
1.3.1 Organizational changes
The total number of sequence data files increased by 30 with this release:
- the BCT division is now comprised of 18 files (+1)
- the EST division is now comprised of 570 files (+16)
- the GSS division is now comprised of 197 files (+7)
- the HTG division is now comprised of 88 files (+2)
- the PAT division is now comprised of 27 files (+1)
- the PLN division is now comprised of 20 files (+1)
- the PRI division is now comprised of 32 files (+1)
- the VRL division is now comprised of 7 files (+1)
Recent problems affecting the generation of the limited non-EST and non-GSS
index files (see Section 1.3.3) have finally been resolved as of GenBank 157.0.
As a result, the number of index files has "increased" by 10 :
- the AUT index is now comprised of 16 files (+8)
- the JOU index is now comprised of 1 files (+1)
- the KEY index is now comprised of 1 files (+1)
1.3.2 Introduction of /mobile_element qualifier
For repeat_region features, the /transposon and /insertion_seq
qualifiers can be used to describe two specific classes of mobile
elements. But not all mobile elements fall into these two categories,
so a new structured /mobile_element qualifier has been introduced
with the GenBank 157.0 release of December 2006.
Here is the definition for /mobile_element, as excerpted from:
http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html#7.4.1
Qualifier /mobile_element=
Definition type and name or identifier of the mobile element which is
described by the parent feature
Value format "<mobile_element_type>[:<mobile_element_name>]" where
mobile_element_type is one of the following:
"transposon", "retrotransposon", "integron",
"insertion sequence", "non-LTR retrotransposon",
"SINE", "MITE", "LINE", "other".
Example /mobile_element="transposon:Tnp9"
Comment /mobile_element is legal on repeat_region feature key only.
Mobile element should be used to represent both elements which
are currently mobile, and those which were mobile in the past.
Value "other" requires a mobile_element_name.
/mobile_element will replace /transposon and /insertion_seq
qualifiers in December 2006
1.3.3 Changes in the content of index files
As described in the GB 153 release notes, the 'index' files which accompany
GenBank releases (see Section 3.3) are considered to be a legacy data product by
NCBI, generated mostly for historical reasons. FTP statistics of January 2005
seem to support this: the index files were transferred only half as frequently as
the files of sequence records. The inherent inefficiencies of the index file
format also lead us to suspect that they have little serious use by the user
community, particularly for EST and GSS records.
The software that generated the index file products received little
attention over the years, and finally reached its limitations in
February 2006 (Release 152.0). The required multi-server queries which
obtained and sorted many millions of rows of terms from several different
databases simply outgrew the capacity of the hardware used for GenBank
Release generation.
Our short-term solution is to cease generating some index-file content
for all EST sequence records, and for GSS sequence records that originate
via direct submission to NCBI. GenBank 157.0 thus contains these index
files, which lack all EST and most GSS content:
gbaut1.idx - gbaut16.idx (16 files)
gbgen.idx
gbjou.idx
gbkey.idx
gbsec.idx
The gbacc.idx index file continues to reflect the entirety of the release,
including all EST and GSS records, however the file's contents are unsorted.
These 'solutions' are really just stop-gaps, and we will likely pursue
one of two options within the next year:
a) Cease support of the 'index' file products altogether.
b) Provide new products that present some of the most useful data from
the legacy 'index' files, and cease support for other types of index data.
If you are a user of the 'index' files associated with GenBank files, we
encourage you to make your wishes known, either via the GenBank newsgroup,
or via email to NCBI's Service Desk:
info At ncbi.nlm.nih.gov
Our apologies for any inconvenience that these changes may cause.
1.3.4 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
thirty-six of the GSS flatfiles in Release 157.0. Consider gbgss162.seq :
GBGSS1.SEQ Genetic Sequence Data Bank
December 15 2006
NCBI-GenBank Flat File Release 157.0
GSS Sequences (Part 1)
86836 loci, 64366786 bases, from 86836 reported sequences
Here, the filename and part number in the header is "1", though the file
has been renamed as "162" 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
(None planned.)
