WormBase release WS163 now online
"WormBase" <[email protected]> Sat, 9 Sep 2006 20:58:34 -0400
| Newsgroups | gmane.science.biology.wormbase.announce |
|---|---|
| Message-ID | <200609100058.k8A0wYdY024979__44917.9449621171$1157850158$gmane$org@brie6.cshl.edu> |
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/WSWS163 New release of WormBase WS163, Wormpep163 and Wormrna163 Thu Aug 17 10:49:02 BST 2006 WS163 was built by Paul Davis [[email protected]] ====================================================================== This directory includes: i) database.WS163.*.tar.gz - compressed data for new release ii) models.wrm.WS163 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS163-WS162.dbcomp - log file reporting difference from last release v) wormpep163.tar.gz - full Wormpep distribution corresponding to WS163 vi) wormrna163.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS163.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS163.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS163.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS163.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS163.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.WS163.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS163.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS163.gz - Mappings between PCR products and overlapping Genes Release notes on the web: ------------------------- http://wwwdev.sanger.ac.uk/Projects/C_elegans/WORMBASE Genome sequence composition: ---------------------------- WS163 WS162 change ---------------------------------------------- a 32365888 32365888 +0 c 17779857 17779855 +2 g 17756012 17756011 +1 t 32365687 32365687 +0 n 0 0 +0 Total 100267444 100267441 +3 Chromosomal Changes: -------------------- Chromosome: III 5953905 5953937 33 -> 5953905 5953940 36 Chromosome: V 20919397 20919396 0 -> 20919397 20919450 54 Gene data set (Live C.elegans genes 23757) ------------------------------------------ Molecular_info 22036 (92.8%) Concise_description 4223 (17.8%) Reference 6322 (26.6%) CGC_approved Gene name 8835 (37.2%) RNAi_result 19804 (83.4%) Microarray_results 19141 (80.6%) SAGE_transcript 0 (0%) Wormpep data set: ---------------------------- There are 20071 CDS in autoace, 23164 when counting 3093 alternate splice forms. The 23164 sequences contain 10,171,003 base pairs in total. Modified entries 18 Deleted entries 7 New entries 16 Reappeared entries 0 Net change +9 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 7775 (33.6%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 10758 (46.4%) Some, but not all exon bases are covered by transcript evidence Predicted 4631 (20.0%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB/Swiss-Prot accessions 3268 (14.1%) UniProtKB/TrEMBL accessions 19611 (84.7%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 22879 (98.8%) Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved) --------------------------------------------- Entries with CGC-approved Gene name 7169 GeneModel correction progress WS162 -> WS163 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 17 | 0 | St Louis | 10 | 5 | +---------+--------+ Members of known repeat families that overlap predicted exons; +---------+--------+ | Repeats | Change | +---------+--------+ Cambridge | 6 | -563 | St Louis | 6 | -740 | +---------+--------+ Synchronisation with GenBank / EMBL: ------------------------------------ CHROMOSOME_III sequence U23172 There are no gaps remaining in the genome sequence --------------- For more info mail [email protected] -===================================================================================- New Data: --------- New Fixes: ---------- SAGE data has been overhauled to allow the data to be more accessible. Known Problems: -------------- Other Changes: -------------- F25B5: 3 bases were added to resolve sequencing errors in to original sequencing project. Proposed Changes / Forthcoming Data: ------------------------------------ Model Changes: ------------------------------------ -===================================================================================- 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. ____________ END _____________