WormBase release WS119 now online
"WormBase" <[email protected]> Sat, 28 Feb 2004 08:32:02 -0500
| Newsgroups | gmane.science.biology.wormbase.announce |
|---|---|
| Message-ID | <200402281332.i1SDW2a02596__43312.3917355717$1077975436@brie6.cshl.org> |
This is an automatic announcement that WormBase
(http://www.wormbase.org) has just been updated. New releases occur
roughly every 2 weeks.
The text of the AceDB release notes, which contains highlights of the
new data is attached. You can download the full AceDB files from:
ftp://ftp.sanger.ac.uk/pub/wormbase/current_release/
New release of WormBase WS119, Wormpep119 and Wormrna119 Fri Feb 13 15:38:16 GMT 2004
WS119 was built by
======================================================================
This directory includes:
i) database.WS119.*.tar.gz - compressed data for new release
ii) models.wrm.WS119 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS119-WS118.dbcomp - log file reporting difference from last release
v) wormpep119.tar.gz - full Wormpep distribution corresponding to WS119
vi) wormrna119.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS119.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) yk2orf.WS119.gz - Latest set of ORF connections to each Yuji Kohara EST clone
ix) gene_interpolated_map_positions.WS119.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS119.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS119.gz - for each C. elegans WormPep protein, lists Best blastp match to
human, fly, yeast, C. briggsae, and SwissProt & Trembl proteins.
xii) best_blastp_hits_brigprot.WS119.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & Trembl proteins.
Release notes on the web:
-------------------------
http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE
Primary databases used in build WS119
------------------------------------
brigdb : 2004-02-02 - updated
camace : 2004-02-02 - updated
citace : 2004-02-01 - updated
cshace : 2003-11-26
genace : 2004-02-05 - updated
stlace : 2004-02-02 - updated
Genome sequence composition:
----------------------------
WS119 WS118 change
----------------------------------------------
a 32368630 32368607 +23
c 17781015 17780992 +23
g 17758448 17758424 +24
t 32369814 32369797 +17
n 8 95 -87
- 0 0 +0
Total 100277915 100277915 +0
Wormpep data set:
----------------------------
There are 19891 CDS in autoace, 22239 when counting 2348 alternate splice forms.
The 22239 sequences contain 9,732,776 base pairs in total.
Modified entries 15
Deleted entries 5
New entries 7
Reappeared entries 0
Net change +2
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 3696 (16.6%) Every base has transcription evidence (mRNA, EST etc )
Partially_confirmed 13145 (59.1%) Some but not all bases are covered by transcript evidence
Predicted 5398 (24.3%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions 2462 (11.1%)
TrEMBL accessions 18476 (83.1%)
TrEMBLnew accessions 1235 (5.6%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 22172 (99.7%)
Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection 4908
GeneModel correction progress WS118 -> WS119
-----------------------------------------
Confirmed introns not is a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 701 | 265 |
St Louis | 527 | 260 |
+---------+--------+
Members of known repeat families that overlap predicted exons;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 0 | 0 |
St Louis | 37 | 0 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
CHROMOSOME_I sequence AC006676
CHROMOSOME_III sequence U40935
CHROMOSOME_IV sequence AC025715
CHROMOSOME_IV sequence AC084158
CHROMOSOME_X sequence AF067215
There are no gaps remaining in the genome sequence
---------------
For more info mail [email protected]
-===================================================================================-
New Data:
---------
87 of the remaining 95 n's in the genomic sequence have been resolved, leaving just 8 to go.
Updated versions of the Gadfly and yeast protein sets were used in the BLAST analyses.
New Fixes:
----------
Known Problems:
--------------
We have had some problems submitting genome sequence files to EMBL so there may be some delay this synchronisation.
This has also meant that any new C.elegans proteins will not yet have a protein id.
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
------------------------------------
The National Bioresources Project of Japan have submitted data for 792 alleles which will be in WS120.
450 TC1 insertion alleles from the Plasterk.
Several genomic sequence corrections will be made for WS120.
An updated waba analysis for elegans vs briggsae will be available in a forthcoming release.
-===================================================================================-
Quick installation guide for UNIX/Linux systems
-----------------------------------------------
1. Create a new directory to contain your copy of WormBase,
e.g. /users/yourname/wormbase
2. Unpack and untar all of the database.*.tar.gz files into
this directory. You will need approximately 2-3 Gb of disk space.
3. Obtain and install a suitable acedb binary for your system
(available from www.acedb.org).
4. Use the acedb 'xace' program to open your database, e.g.
type 'xace /users/yourname/wormbase' at the command prompt.
5. See the acedb website for more information about acedb and
using xace.
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