Difference between revisions of "WS142"
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Revision as of 20:40, 17 August 2010
Contents
Release Letter
New release of WormBase WS142, Wormpep142 and Wormrna142 Fri Apr 15 18:22:51 BST 2005 WS142 was built by Paul Davis ====================================================================== This directory includes: i) database.WS142.*.tar.gz - compressed data for new release ii) models.wrm.WS142 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS142-WS141.dbcomp - log file reporting difference from last release v) wormpep142.tar.gz - full Wormpep distribution corresponding to WS142 vi) wormrna142.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS142.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS142.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS142.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS142.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS142.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.WS142.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS142.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS142.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 WS142 ------------------------------------ brigdb : 2004-03-12 camace : 2005-03-29 - updated citace : 2005-03-25 - updated cshace : 2005-03-07 genace : 2005-03-29 - updated stlace : 2005-03-25 - updated Genome sequence composition: ---------------------------- WS142 WS141 change ---------------------------------------------- a 32366710 32365928 +782 c 17780361 17779940 +421 g 17756435 17756857 -422 t 32366406 32367188 -782 n 0 0 +0 - 0 0 +0 Total 100269912 100269913 -1 Gene data set (Live C.elegans genes 23624) ------------------------------------------ Molecular_info 21816 (92.3%) Concise_description 3933 (16.6%) Reference 4106 (17.3%) CGC_approved Gene name 7658 (32.4%) RNAi_result 19707 (83.4%) Microarray_results 18255 (77.2%) SAGE_transcript 18312 (77.5%) Wormpep data set: ---------------------------- There are 19851 CDS in autoace, 22608 when counting 2757 alternate splice forms. The 22608 sequences contain 10,006,658 base pairs in total. Modified entries 45 Deleted entries 39 New entries 209 Reappeared entries 2 Net change +172 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 6389 (28.3%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 11470 (50.7%) Some, but not all exon bases are covered by transcript evidence Predicted 4749 (21.0%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- Swissprot accessions 21146 (93.5%) TrEMBL accessions 13 (0.1%) TrEMBLnew accessions 3 (0.0%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 21219 (93.9%) Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved) --------------------------------------------- Entries with CGC-approved Gene name 5917 GeneModel correction progress WS141 -> WS142 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 178 | -77 | St Louis | 30 | -8 | +---------+--------+ Members of known repeat families that overlap predicted exons; +---------+--------+ | Repeats | Change | +---------+--------+ Cambridge | 613 | 40 | St Louis | 847 | 75 | +---------+--------+ Synchronisation with GenBank / EMBL: ------------------------------------ CHROMOSOME_I sequence AF067211 CHROMOSOME_I sequence AF067211 CHROMOSOME_I sequence AF067211 CHROMOSOME_X sequence Z92839 There are no gaps remaining in the genome sequence --------------- For more info mail worm@sanger.ac.uk -===================================================================================- New Data: --------- A)The Genome sequence has changed for WS142: 1)T08D2 has been inverted to resolve a missasenbly. 2)C14B9 has a single deletion following a sequence error correction. B)Some of the RNAi datasets (including the latest set from Tony Hyman) have multiple RNAi mappings to indicate primary and secondary placing on the genome. This allows WormBase to better indicate RNAi experiments which interfere with multipletargets in the genome. New Fixes: ---------- Known Problems: -------------- Other Changes: -------------- Proposed Changes / Forthcoming Data: ------------------------------------ -===================================================================================- 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 _____________