Difference between revisions of "WS147"
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Latest revision as of 11:09, 21 December 2011
Contents
Release Letter
New release of WormBase WS147, Wormpep147 and Wormrna147 Thu Aug 18 16:59:45 BST 2005 WS147 was built by Paul Davis ====================================================================== This directory includes: i) database.WS147.*.tar.gz - compressed data for new release ii) models.wrm.WS147 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS147-WS146.dbcomp - log file reporting difference from last release v) wormpep147.tar.gz - full Wormpep distribution corresponding to WS147 vi) wormrna147.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS147.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS147.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS147.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS147.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS147.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.WS147.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS147.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS147.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 WS147 ------------------------------------ brigdb : 2004-03-12 camace : 2005-08-01 - updated citace : 2005-07-29 - updated cshace : 2005-03-07 genace : 2005-08-01 - updated stlace : 2005-07-29 - updated Genome sequence composition: ---------------------------- WS147 WS146 change ---------------------------------------------- a 32366710 32366710 +0 c 17780361 17780361 +0 g 17756436 17756436 +0 t 32366406 32366406 +0 n 0 0 +0 - 0 0 +0 Total 100269913 100269913 +0 Gene data set (Live C.elegans genes 23919) ------------------------------------------ Molecular_info 22111 (92.4%) Concise_description 4091 (17.1%) Reference 4644 (19.4%) CGC_approved Gene name 8191 (34.2%) RNAi_result 19783 (82.7%) Microarray_results 19118 (79.9%) SAGE_transcript 18300 (76.5%) Wormpep data set: ---------------------------- There are 20055 CDS in autoace, 22806 when counting 2751 alternate splice forms. The 22806 sequences contain 10,023,921 base pairs in total. Modified entries 41 Deleted entries 24 New entries 28 Reappeared entries 1 Net change +5 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 6445 (28.3%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 11414 (50.0%) Some, but not all exon bases are covered by transcript evidence Predicted 4947 (21.7%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- Swissprot accessions 2945 (12.9%) TrEMBL accessions 19532 (85.6%) TrEMBLnew accessions 0 (0.0%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 22477 (98.6%) Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved) --------------------------------------------- Entries with CGC-approved Gene name 6449 GeneModel correction progress WS146 -> WS147 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 186 | -1 | St Louis | 82 | -10 | +---------+--------+ Members of known repeat families that overlap predicted exons; +---------+--------+ | Repeats | Change | +---------+--------+ Cambridge | 593 | -3 | St Louis | 794 | -5 | +---------+--------+ Synchronisation with GenBank / EMBL: ------------------------------------ CHROMOSOME_I sequence AL032679 CHROMOSOME_I sequence AC024206 CHROMOSOME_I sequence AC024796 CHROMOSOME_I sequence AF003139 CHROMOSOME_II sequence AL590344 CHROMOSOME_II sequence AL032669 CHROMOSOME_II sequence AF025458 CHROMOSOME_II sequence AF024493 CHROMOSOME_II sequence U80453 CHROMOSOME_III sequence AL031226 CHROMOSOME_III sequence AF078783 CHROMOSOME_III sequence AF040660 CHROMOSOME_III sequence AF099913 CHROMOSOME_IV sequence AL032676 CHROMOSOME_IV sequence AC006742 CHROMOSOME_IV sequence AF067615 CHROMOSOME_IV sequence AF078781 CHROMOSOME_V sequence AL031270 CHROMOSOME_V sequence AF068714 CHROMOSOME_V sequence AC006744 CHROMOSOME_V sequence AF101312 CHROMOSOME_X sequence AL031272 CHROMOSOME_X sequence AL954368 CHROMOSOME_X sequence AL954365 CHROMOSOME_X sequence BX000427 There are no gaps remaining in the genome sequence --------------- For more info mail help@wormbase.org -===================================================================================- New Data: --------- 1) Large increase in Microarray_results due to recent publications. New Fixes: ---------- 1) Variation schema and data was out of sync for WS146, this has been partially resolved for WS147 by grouping Description tags and info under a Pheynotype_remark tag. This will be fully resolved for WS148 as the model is being rolled back while curators get to work representing this data as Phenotype objects. Known Problems: -------------- Other Changes: -------------- Proposed Changes / Forthcoming Data: ------------------------------------ 1) New Expression_cluster class to replace Cluster to represent microarray result clusters. Forthcoming Model Changes: -------------------------- 1) Expression_cluster model. -===================================================================================- 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 _____________