WormBase release WS156 now online
"WormBase" <[email protected]> Tue, 18 Apr 2006 08:36:42 -0400
| Newsgroups | gmane.science.biology.wormbase.announce,gmane.science.biology.wormbase.general |
|---|---|
| Message-ID | <[email protected]> |
This is an automatic announcement that WormBase
(http://www.wormbase.org) has just been updated. New releases occur
roughly every three 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/
or
ftp://ftp.wormbase.org/pub/wormbase/acedb/current_release
Additional information on the release, including any necessary patches or bug
fixes can be found on the WormBaseWiki:
http://www.wormbase.org/wiki/index.php/WSWS156
New release of WormBase WS156, Wormpep156 and Wormrna156 Fri Mar 24 13:00:23 GMT 2006
WS156 was built by Mary Ann
======================================================================
This directory includes:
i) database.WS156.*.tar.gz - compressed data for new release
ii) models.wrm.WS156 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS156-WS155.dbcomp - log file reporting difference from last release
v) wormpep156.tar.gz - full Wormpep distribution corresponding to WS156
vi) wormrna156.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS156.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS156.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS156.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS156.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS156.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.WS156.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS156.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS156.gz - Mappings between PCR products and overlapping Genes
Release notes on the web:
-------------------------
http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE
Primary databases used in build WS156
------------------------------------
brigdb : 2004-03-12
camace : 2006-03-03 - updated
citace : 2006-03-03 - updated
cshace : 2005-11-04
geneace : 2006-03-03 - updated
stlace : 2006-03-03 - updated
Genome sequence composition:
----------------------------
WS156 WS155 change
----------------------------------------------
a 32365775 32365775 +0
c 17779813 17779813 +0
g 17755968 17755968 +0
t 32365578 32365578 +0
n 0 0 +0
Total 100267134 100267134 +0
Chromosomal Changes:
--------------------
There are no changes to the chromosome sequences in this release.
Gene data set (Live C.elegans genes 23742)
------------------------------------------
Molecular_info 21992 (92.6%)
Concise_description 4157 (17.5%)
Reference 4989 (21%)
CGC_approved Gene name 8737 (36.8%)
RNAi_result 19793 (83.4%)
Microarray_results 19113 (80.5%)
SAGE_transcript 18191 (76.6%)
Wormpep data set:
----------------------------
There are 20083 CDS in autoace, 23086 when counting 3003 alternate splice forms.
The 23086 sequences contain 10,137,871 base pairs in total.
Modified entries 78
Deleted entries 36
New entries 79
Reappeared entries 0
Net change +43
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 6633 (28.7%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 11438 (49.5%) Some, but not all exon bases are covered by transcript evidence
Predicted 5015 (21.7%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions 3176 (13.8%)
UniProtKB/TrEMBL accessions 19527 (84.6%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 22703 (98.3%)
Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name 7049
GeneModel correction progress WS155 -> WS156
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 99 | 99 |
St Louis | 8 | 8 |
+---------+--------+
Members of known repeat families that overlap predicted exons;
+---------+--------+
| Repeats | Change |
+---------+--------+
Cambridge | 580 | 580 |
St Louis | 750 | 750 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
No synchronisation issues
There are no gaps remaining in the genome sequence
---------------
For more info mail [email protected]
-===================================================================================-
New Data:
---------
Updated databases for BLAST analyses :
IPI_human
New Fixes:
----------
Known Problems:
--------------
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
------------------------------------
Model Changes:
------------------------------------
1) #GR_condition : "Type" tag added to distinguish regulation of expression level or localization.
"Regulation_level" tag added to distinguish whether the regulation happens at transcriptional, post-transcriptional,
and post-translational level.
2) ?Variation : "SeqStatus" tag added as a way to differentiate between mutations which have been sequenced
and those which have not.
3) ?Variation : #Molecular_change added to allow detailed description of how variations affect Genes, CDSs etc.
-===================================================================================-
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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