WormBase release WS155 now online
"WormBase" <[email protected]> Sun, 26 Mar 2006 12:37:40 -0500
| 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/WSWS155
New release of WormBase WS155, Wormpep155 and Wormrna155 Fri Mar 3 14:51:02 GMT 2006
WS155 was built by [INSERT NAME HERE]
======================================================================
This directory includes:
i) database.WS155.*.tar.gz - compressed data for new release
ii) models.wrm.WS155 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS155-WS154.dbcomp - log file reporting difference from last release
v) wormpep155.tar.gz - full Wormpep distribution corresponding to WS155
vi) wormrna155.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS155.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS155.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS155.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS155.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS155.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.WS155.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS155.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS155.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 WS155
------------------------------------
camace : 2006-02-10 - updated
genace : 2006-02-10 - updated
citace : 2006-02-10 - updated
stlace : 2006-02-10 - updated
cshace : 2006-02-10 - updated
brigdb : 2004-03-12
Genome sequence composition:
----------------------------
WS155 WS154 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 23718)
------------------------------------------
Molecular_info 21968 (92.6%)
Concise_description 4151 (17.5%)
Reference 4980 (21%)
CGC_approved Gene name 8730 (36.8%)
RNAi_result 20497 (86.4%)
Microarray_results 17436 (73.5%)
SAGE_transcript 18196 (76.7%)
Wormpep data set:
----------------------------
There are 20070 CDS in autoace, 23043 when counting 2973 alternate splice forms.
The 23043 sequences contain 10,116,737 base pairs in total.
Modified entries 126
Deleted entries 81
New entries 177
Reappeared entries 4
Net change +100
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 6617 (28.7%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 11428 (49.6%) Some, but not all exon bases are covered by transcript evidence
Predicted 4998 (21.7%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions 3176 (13.8%)
UniProtKB/TrEMBL accessions 19567 (84.9%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 22743 (98.7%)
Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name 7041
Synchronisation with GenBank / EMBL:
------------------------------------
No synchronisation issues
There are no gaps remaining in the genome sequence
---------------
For more info mail [email protected]
-===================================================================================-
New Data:
---------
The following BLAST databases have been updated
UniProt-Swissprot 49
UniProt-TrEMBL 32
New Fixes:
----------
C.elegans vs C.briggsae waba analysis and Twinscan gene predictions have been updated due to previous genome sequence changes.
A bug in the UTR generation code has been fixed. This previously caused the aggregation of some CDSs and Coding_transcripts to go wrong
The interpolation of genetic map positions for Vancouver fosmids has been corrected.
Known Problems:
--------------
The "confirmed introns not in gene model" and related stats are not included in this note but will return in the future
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
------------------------------------
Model Changes:
------------------------------------
added split and merge tags to CDS for StLouis and removed UNIQUE from the RNAi Database line so that multiple connections to the same database can be made
-===================================================================================-
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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