Difference between revisions of "WS205"
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Revision as of 09:06, 22 July 2009
Release Letter
New release of WormBase WS205, Wormpep205 and Wormrna205 Wed Jul 22 10:29:27 BST 2009 WS205 was built by Michael Han (<mh6@sanger.ac.uk>) ====================================================================== This directory includes: i) database.WS205.*.tar.gz - compressed data for new release ii) models.wrm.WS205 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS205-WS204.dbcomp - log file reporting difference from last release v) wormpep205.tar.gz - full Wormpep distribution corresponding to WS205 vi) wormrna205.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS205.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS205.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS205.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS205.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS205.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.WS205.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS205.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS205.gz - Mappings between PCR products and overlapping Genes Release notes on the web: ------------------------- http://www.wormbase.org/wiki/index.php/Release_Schedule Genome sequence composition: ---------------------------- WS205 WS204 change ---------------------------------------------- a 32367418 32367418 +0 c 17780763 17780763 +0 g 17756943 17756943 +0 t 32367086 32367086 +0 n 0 0 +0 - 0 0 +0 Total 100272210 100272210 +0 Chromosomal Changes: -------------------- There are no changes to the chromosome sequences in this release. Gene data set (Live C.elegans genes 39951) ------------------------------------------ Molecular_info 38244 (95.7%) Concise_description 5592 (14%) Reference 13539 (33.9%) WormBase_approved Gene name 25815 (64.6%) RNAi_result 22803 (57.1%) Microarray_results 21047 (52.7%) SAGE_transcript 19028 (47.6%) Wormpep data set: ---------------------------- There are 20197 CDS in autoace, 24114 when counting 3917 alternate splice forms. The 24114 sequences contain 10,659,313 base pairs in total. Modified entries 59 Deleted entries 44 New entries 106 Reappeared entries 0 Net change +62 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 9790 (40.6%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 11535 (47.8%) Some, but not all exon bases are covered by transcript evidence Predicted 2789 (11.6%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB accessions 23966 (99.4%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 23966 (99.4%) Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis elegans entries with WormBase-approved Gene name 24156 GeneModel correction progress WS204 -> WS205 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 0 | 0 | St Louis | 0 | 0 | +---------+--------+ Members of known repeat families that overlap predicted exons; +---------+--------+ | Repeats | Change | +---------+--------+ Cambridge | 0 | 0 | St Louis | 0 | 0 | +---------+--------+ Synchronisation with GenBank / EMBL: ------------------------------------ No synchronisation issues There are no gaps remaining in the genome sequence --------------- For more info mail worm@sanger.ac.uk -===================================================================================- New Data: --------- * new and updated data from the C.elegans Gene Knockout Consortium * new and updated knockout data from the National BioResource Project (NBRP) * Meloidogyne incognita genome added to WormBase as Tier III species * Paralog predictions added to Tier I/II species genes from wormbase-compara * updated C.elegans and C.brenneri databases Genome sequence updates: ----------------------- New Fixes: ---------- Known Problems: --------------- Other Changes: -------------- Proposed Changes / Forthcoming Data: ------------------------------------- * Operon updates for chromosome I/II/X based on modEncode/Waterstone short read data * Orthology Matrix (OMA) updates from ETH Zurich * repeat library updates for Tier II species from Ismael Vergara (Jack Chen lab) * potential Caenorhabditis japonica genome assembly changes (WashU) * Heterorhabditis bacteriophora genome 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 20-30 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 _____________