WS173
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Release Notes
New release of WormBase WS173, Wormpep173 and Wormrna173 Fri Mar 23 18:22:22 GMT 2007 WS173 was built by Michael Han ====================================================================== This directory includes: i) database.WS173.*.tar.gz - compressed data for new release ii) models.wrm.WS173 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS173-WS172.dbcomp - log file reporting difference from last release v) wormpep173.tar.gz - full Wormpep distribution corresponding to WS173 vi) wormrna173.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS173.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS173.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS173.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS173.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS173.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.WS173.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS173.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS173.gz - Mappings between PCR products and overlapping Genes Release notes on the web: ------------------------- http://www.wormbase.org/wiki/index.php/Release_notes Genome sequence composition: ---------------------------- WS173 WS172 change ---------------------------------------------- a 32365889 32365889 +0 c 17779856 17779856 +0 g 17756016 17756016 +0 t 32365689 32365689 +0 n 0 0 +0 Total 100267450 100267450 +0 Chromosomal Changes: -------------------- There are no changes to the chromosome sequences in this release. Gene data set (Live C.elegans genes 24019) ------------------------------------------ Molecular_info 22327 (93%) Concise_description 4474 (18.6%) Reference 6939 (28.9%) CGC_approved Gene name 9084 (37.8%) RNAi_result 19856 (82.7%) Microarray_results 19143 (79.7%) SAGE_transcript 20048 (83.5%) there are 20106 CDS in autoace, 23258 when counting (3152) alternate splice_forms Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 7805 (33.6%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 10840 (46.6%) Some, but not all exon bases are covered by transcript evidence Predicted 4613 (19.8%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB/Swiss-Prot accessions 3504 (15.1%) UniProtKB/TrEMBL accessions 19421 (83.5%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 22898 (98.5%) Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved) --------------------------------------------- Entries with CGC-approved Gene name 7443 GeneModel correction progress WS172 -> WS173 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 184 | -1 | St Louis | 215 | 1 | +---------+--------+ Members of known repeat families that overlap predicted exons; +---------+--------+ | Repeats | Change | +---------+--------+ Cambridge | 6 | 0 | St Louis | 6 | 0 | +---------+--------+ Synchronisation with GenBank / EMBL: ------------------------------------ No synchronisation issues There are no gaps remaining in the genome sequence --------------- For more info mail worm@sanger.ac.uk -===================================================================================- New Data: --------- * added Nemagenetag dbinfo for crossreferencing with the Nemagene website * Deletion_validation data added to variations to show additional experimental evidence Genome sequence updates: ----------------------- * change of ownership for some genomic clones between WashU and Sanger New Fixes: ---------- Known Problems: --------------- Other Changes: -------------- Proposed Changes / Forthcoming Data: ------------------------------------- Model Changes: ------------------------------------ * made Reference UNIQUE in RNAi class -===================================================================================- 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.