WormBase release WS141 now online
"WormBase" <[email protected]> Tue, 19 Apr 2005 14:13:32 -0400
| Newsgroups | gmane.science.biology.wormbase.announce |
|---|---|
| Message-ID | <200504191813.j3JIDW9F018659__21311.2894482494$1113934390$gmane$org@brie6.cshl.org> |
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/elegans/current_release
New release of WormBase WS141, Wormpep141 and Wormrna141 Wed Mar 23 16:18:12 GMT 2005
WS141 was built by Mary Ann
======================================================================
This directory includes:
i) database.WS141.*.tar.gz - compressed data for new release
ii) models.wrm.WS141 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS141-WS140.dbcomp - log file reporting difference from last release
v) wormpep141.tar.gz - full Wormpep distribution corresponding to WS141
vi) wormrna141.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS141.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS141.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS141.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS141.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS141.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.WS141.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS141.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS141.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 WS141
------------------------------------
brigdb : 2004-03-12
camace : 2005-03-08 - updated
citace : 2005-03-04 - updated
cshace : 2005-03-07 - updated
genace : 2005-03-08 - updated
stlace : 2005-03-04 - updated
Genome sequence composition:
----------------------------
WS141 WS140 change
----------------------------------------------
a 32365928 32368572 -2644
c 17779940 17781252 -1312
g 17756857 17758265 -1408
t 32367188 32369957 -2769
n 0 0 +0
- 0 0 +0
Total 100269913 100278046 -8133
Gene data set (Live C.elegans genes 23569)
------------------------------------------
Molecular_info 21669 (91.9%)
Concise_description 3921 (16.6%)
Reference 4099 (17.4%)
CGC_approved Gene name 7651 (32.5%)
RNAi_result 16508 (70.0%)
Microarray_results 18236 (77.4%)
SAGE_transcript 18313 (77.7%)
Wormpep data set:
----------------------------
There are 19729 CDS in autoace, 22436 when counting 2707 alternate splice forms.
The 22436 sequences contain 9,957,916 base pairs in total.
Modified entries 100
Deleted entries 42
New entries 57
Reappeared entries 1
Net change +16
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 6342 (28.3%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 11444 (51.0%) Some, but not all exon bases are covered by transcript evidence
Predicted 4650 (20.7%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions 21452 (95.6%)
TrEMBL accessions 4 (0.0%)
TrEMBLnew accessions 0 (0.0%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 21493 (95.8%)
Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name 5906
GeneModel correction progress WS140 -> WS141
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 255 | -6 |
St Louis | 38 | 2 |
+---------+--------+
Members of known repeat families that overlap predicted exons;
+---------+--------+
| Repeats | Change |
+---------+--------+
Cambridge | 573 | -6 |
St Louis | 772 | 2 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
No synchronisation issues
There are no gaps remaining in the genome sequence
---------------
For more info mail [email protected]
-===================================================================================-
New Data:
---------
Incorporation of the latest RNAi data set from Tony Hyman (21,300 experiments)
New Fixes:
----------
Known Problems:
--------------
Other Changes:
--------------
Genome sequence modified to remove an 8.1 kb duplicated region on chromosome I.
Proposed Changes / Forthcoming Data:
------------------------------------
RNAi mappings to indicate primary and secondary placing on the genome. This will
allow WormBase to better indicate RNAi experiments which interfere with multiple
targets in the genome.
New gene predictions based on analysis of novel Genefinder and Twinscan predictions.
-===================================================================================-
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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