WS146
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Release Letter
New release of WormBase WS146, Wormpep146 and Wormrna146 Thu Jul 28 14:01:21 BST 2005 WS146 was built by Paul Davis ====================================================================== This directory includes: i) database.WS146.*.tar.gz - compressed data for new release ii) models.wrm.WS146 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS146-WS145.dbcomp - log file reporting difference from last release v) wormpep146.tar.gz - full Wormpep distribution corresponding to WS146 vi) wormrna146.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS146.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS146.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS146.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS146.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS146.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.WS146.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS146.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS146.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 WS146 ------------------------------------ brigdb : 2004-03-12 camace : 2005-07-08 - updated citace : 2005-07-05 - updated cshace : 2005-03-07 genace : 2005-07-08 - updated stlace : 2005-06-22 - updated Genome sequence composition: ---------------------------- WS146 WS145 change ---------------------------------------------- a 32366710 32366710 +0 c 17780361 17780361 +0 g 17756436 17756435 +1 t 32366406 32366406 +0 n 0 0 +0 - 0 0 +0 Total 100269913 100269912 +1 Total number of bases has increased - due to the resolution of a single base sequencing error. Gene data set (Live C.elegans genes 23925) ------------------------------------------ Molecular_info 22112 (92.4%) Concise_description 4064 (17%) Reference 4232 (17.7%) CGC_approved Gene name 7980 (33.4%) RNAi_result 19796 (82.7%) Microarray_results 18262 (76.3%) SAGE_transcript 18311 (76.5%) Wormpep data set: ---------------------------- There are 20063 CDS in autoace, 22801 when counting 2738 alternate splice forms. The 22801 sequences contain 10,013,507 base pairs in total. Modified entries 15 Deleted entries 104 New entries 152 Reappeared entries 23 Net change +71 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 6439 (28.2%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 11413 (50.1%) Some, but not all exon bases are covered by transcript evidence Predicted 4949 (21.7%) No transcriptional evidence at all Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 22295 (97.8%) Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved) --------------------------------------------- Entries with CGC-approved Gene name 6236 GeneModel correction progress WS145 -> WS146 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 187 | 49 | St Louis | 92 | 69 | +---------+--------+ Members of known repeat families that overlap predicted exons; +---------+--------+ | Repeats | Change | +---------+--------+ Cambridge | 596 | -1 | St Louis | 799 | -31 | +---------+--------+ Synchronisation with GenBank / EMBL: ------------------------------------ CHROMOSOME_III sequence L13200 There are no gaps remaining in the genome sequence --------------- For more info mail worm@sanger.ac.uk -===================================================================================- New Data: --------- + 1bp insertion into ZK1236. Model Changes: -------------- + Updates for Phenotype in Variation and Transgene, + Genomic tag to Sequence model, + Ignore tag to Transcript model, + Updates to Structure_data model, 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 _____________