Difference between revisions of "WS171"
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Revision as of 20:42, 17 August 2010
New release of WormBase WS171, Wormpep171 and Wormrna171 Thu Feb 8 15:28:27 GMT 2007 WS171 was built by Anthony ====================================================================== This directory includes: i) database.WS171.*.tar.gz - compressed data for new release ii) models.wrm.WS171 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS171-WS170.dbcomp - log file reporting difference from last release v) wormpep171.tar.gz - full Wormpep distribution corresponding to WS171 vi) wormrna171.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS171.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS171.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS171.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS171.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS171.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.WS171.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS171.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS171.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: ---------------------------- WS171 WS170 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 23967) ------------------------------------------ Molecular_info 22274 (92.9%) Concise_description 4401 (18.4%) Reference 6731 (28.1%) CGC_approved Gene name 8945 (37.3%) RNAi_result 19843 (82.8%) Microarray_results 19135 (79.8%) SAGE_transcript 20061 (83.7%) Wormpep data set: ---------------------------- There are 20085 CDS in autoace, 23226 when counting 3141 alternate splice forms. The 23226 sequences contain 10,187,058 base pairs in total. Modified entries 6 Deleted entries 4 New entries 3 Reappeared entries 3 Net change +2 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 7825 (33.7%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 10745 (46.3%) Some, but not all exon bases are covered by transcript evidence Predicted 4656 (20.0%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB/Swiss-Prot accessions 3489 (15.0%) UniProtKB/TrEMBL accessions 19365 (83.4%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 22854 (98.4%) Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved) --------------------------------------------- Entries with CGC-approved Gene name 7303 GeneModel correction progress WS170 -> WS171 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 15 | 0 | St Louis | 13 | 3 | +---------+--------+ 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: --------- C.remanei orthologs assignments are now made using the WashU preliminary gene set. Syntenic alignments of the genome sequence are still included in the compara download. Genome sequence updates: ----------------------- none New Fixes: ---------- Known Problems: --------------- Other Changes: -------------- Proposed Changes / Forthcoming Data: ------------------------------------- Model Changes: ------------------------------------ none -===================================================================================- 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 _____________