Difference between revisions of "WS175"
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There are no gaps remaining in the genome sequence | There are no gaps remaining in the genome sequence | ||
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− | For more info mail | + | For more info mail help@wormbase.org |
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Latest revision as of 10:54, 21 December 2011
New release of WormBase WS175, Wormpep175 and Wormrna175 Fri May 4 16:29:43 BST 2007 WS175 was built by [Anthony] ====================================================================== This directory includes: i) database.WS175.*.tar.gz - compressed data for new release ii) models.wrm.WS175 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS175-WS174.dbcomp - log file reporting difference from last release v) wormpep175.tar.gz - full Wormpep distribution corresponding to WS175 vi) wormrna175.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS175.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS175.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS175.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS175.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS175.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.WS175.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS175.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS175.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: ---------------------------- WS175 WS174 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 24085) ------------------------------------------ Molecular_info 22393 (93%) Concise_description 4579 (19%) Reference 7004 (29.1%) CGC_approved Gene name 9177 (38.1%) RNAi_result 19871 (82.5%) Microarray_results 19149 (79.5%) SAGE_transcript 20043 (83.2%) Wormpep data set: ---------------------------- There are 20115 CDS in autoace, 23273 when counting 3158 alternate splice forms. The 23273 sequences contain 10,219,495 base pairs in total. Modified entries 42 Deleted entries 8 New entries 21 Reappeared entries 2 Net change +15 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 7866 (33.8%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 10792 (46.4%) Some, but not all exon bases are covered by transcript evidence Predicted 4615 (19.8%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB/Swiss-Prot accessions 3496 (15.0%) UniProtKB/TrEMBL accessions 19225 (82.6%) GeneModel correction progress WS174 -> WS175 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 173 | -13 | St Louis | 212 | -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 help@wormbase.org -===================================================================================- New Data: --------- Database cross references to miRBase have been added to 131 genes. Genome sequence updates: ----------------------- New Fixes: ---------- Known Problems: --------------- Other Changes: -------------- Proposed Changes / Forthcoming Data: ------------------------------------- Model Changes: ------------------------------------ Added tags to ?Person and ?Paper to enable recording of negative connections ie Mr X did NOT contribue to this paper. Added Map_evidence to ?Transgene so that the paper that mapping data is taken from can be attributed Added a tags to ?Expr_pattern and  ?Expression_cluster to handle Localizome data Changes in the ?Interaction model as proposed by Andrei. Added #Interactor_info and #Interaction_info Directed_Y1H in YH 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. ____________ END _____________