WS131
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Release Letter
New release of WormBase WS131, Wormpep131 and Wormrna131 Tue Sep 7 15:06:49 BST 2004 WS131 was built by Paul Davis ====================================================================== This directory includes: i) database.WS131.*.tar.gz - compressed data for new release ii) models.wrm.WS131 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS131-WS130.dbcomp - log file reporting difference from last release v) wormpep131.tar.gz - full Wormpep distribution corresponding to WS131 vi) wormrna131.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS131.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) yk2orf.WS131.gz - Latest set of ORF connections to each Yuji Kohara EST clone ix) gene_interpolated_map_positions.WS131.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS131.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS131.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.WS131.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS131.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS131.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 WS131 ------------------------------------ brigdb : 2004-03-12 camace : 2004-08-24 - updated citace : 2004-08-16 - updated cshace : 2004-05-10 genace : 2004-09-01 - updated stlace : 2004-08-16 - updated Genome sequence composition: ---------------------------- WS131 WS130 change ---------------------------------------------- a 32368573 32368573 +0 c 17781252 17781252 +0 g 17758265 17758265 +0 t 32369957 32369957 +0 n 0 0 +0 - 0 0 +0 Total 100278047 100278047 +0 Wormpep data set: ---------------------------- There are 19766 CDS in autoace, 22297 when counting 2531 alternate splice forms. The 22297 sequences contain 9,842,631 base pairs in total. Modified entries 73 Deleted entries 50 New entries 96 Reappeared entries 1 Net change +47The differnce between the total CDS's of this (22297) and the last build (22249) does not equal the net change 47 Please investigate! ! Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 5615 (25.2%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 10919 (49.0%) Some, but not all exon bases are covered by transcript evidence Predicted 5763 (25.8%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- Swissprot accessions 2711 (12.2%) TrEMBL accessions 19262 (86.4%) TrEMBLnew accessions 0 (0.0%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 22178 (99.5%) Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved) --------------------------------------------- Entries with CGC-approved Gene name 5214 GeneModel correction progress WS130 -> WS131 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 519 | -274 | St Louis | 209 | -343 | +---------+--------+ Members of known repeat families that overlap predicted exons; +---------+--------+ | Repeats | Change | +---------+--------+ Cambridge | 604 | -4 | St Louis | 830 | -1 | +---------+--------+ Synchronisation with GenBank / EMBL: ------------------------------------ CHROMOSOME_II sequence U39471 There are no gaps remaining in the genome sequence --------------- For more info mail help@wormbase.org -===================================================================================- New Data: --------- Updated IPI human protein set included in this build. New Fixes: ---------- Known problems documented in the WS130 release letter have been resolved. Known Problems: -------------- Other Changes: -------------- Proposed Changes / Forthcoming Data: ------------------------------------ SRZ family update. Update to the ortholog assignments for elegans CDS <-> briggsae CDS. -===================================================================================- 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 _____________