Difference between revisions of "WS163"
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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 10:57, 21 December 2011
Contents
Release Letter
New release of WormBase WS163, Wormpep163 and Wormrna163 Thu Aug 17 10:49:02 BST 2006 WS163 was built by Paul Davis [paul.davis@wormbase.org] ====================================================================== This directory includes: i) database.WS163.*.tar.gz - compressed data for new release ii) models.wrm.WS163 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS163-WS162.dbcomp - log file reporting difference from last release v) wormpep163.tar.gz - full Wormpep distribution corresponding to WS163 vi) wormrna163.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS163.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS163.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS163.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS163.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS163.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.WS163.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS163.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS163.gz - Mappings between PCR products and overlapping Genes Release notes on the web: ------------------------- http://wwwdev.sanger.ac.uk/Projects/C_elegans/WORMBASE Genome sequence composition: ---------------------------- WS163 WS162 change ---------------------------------------------- a 32365888 32365888 +0 c 17779857 17779855 +2 g 17756012 17756011 +1 t 32365687 32365687 +0 n 0 0 +0 Total 100267444 100267441 +3 Chromosomal Changes: -------------------- Chromosome: III 5953905 5953937 33 -> 5953905 5953940 36 Chromosome: V 20919397 20919396 0 -> 20919397 20919450 54 Gene data set (Live C.elegans genes 23757) ------------------------------------------ Molecular_info 22036 (92.8%) Concise_description 4223 (17.8%) Reference 6322 (26.6%) CGC_approved Gene name 8835 (37.2%) RNAi_result 19804 (83.4%) Microarray_results 19141 (80.6%) SAGE_transcript 0 (0%) Wormpep data set: ---------------------------- There are 20071 CDS in autoace, 23164 when counting 3093 alternate splice forms. The 23164 sequences contain 10,171,003 base pairs in total. Modified entries 18 Deleted entries 7 New entries 16 Reappeared entries 0 Net change +9 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 7775 (33.6%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 10758 (46.4%) Some, but not all exon bases are covered by transcript evidence Predicted 4631 (20.0%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB/Swiss-Prot accessions 3268 (14.1%) UniProtKB/TrEMBL accessions 19611 (84.7%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 22879 (98.8%) Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved) --------------------------------------------- Entries with CGC-approved Gene name 7169 GeneModel correction progress WS162 -> WS163 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 17 | 0 | St Louis | 10 | 5 | +---------+--------+ Members of known repeat families that overlap predicted exons; +---------+--------+ | Repeats | Change | +---------+--------+ Cambridge | 6 | -563 | St Louis | 6 | -740 | +---------+--------+ Synchronisation with GenBank / EMBL: ------------------------------------ CHROMOSOME_III sequence U23172 There are no gaps remaining in the genome sequence --------------- For more info mail help@wormbase.org -===================================================================================- New Data: --------- New Fixes: ---------- SAGE data has been overhauled to allow the data to be more accessible. Known Problems: -------------- Other Changes: -------------- F25B5: 3 bases were added to resolve sequencing errors in to original sequencing project. Proposed Changes / Forthcoming Data: ------------------------------------ Model Changes: ------------------------------------ -===================================================================================- 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 _____________