Difference between revisions of "WS209"
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Latest revision as of 16:50, 21 December 2011
Release Notes
New release of WormBase WS209, Wormpep209 and Wormrna209 Fri Nov 27 11:57:36 GMT 2009 WS209 was built by [Michael Han] ====================================================================== This directory includes: i) database.WS209.*.tar.gz - compressed data for new release ii) models.wrm.WS209 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS209-WS208.dbcomp - log file reporting difference from last release v) wormpep209.tar.gz - full Wormpep distribution corresponding to WS209 vi) wormrna209.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS209.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS209.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS209.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS209.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS209.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.WS209.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS209.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS209.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: ---------------------------- WS209 WS208 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 40034) ------------------------------------------ Molecular_info 38329 (95.7%) Concise_description 5612 (14%) Reference 13654 (34.1%) WormBase_approved Gene name 25848 (64.6%) RNAi_result 24271 (60.6%) Microarray_results 21060 (52.6%) SAGE_transcript 19063 (47.6%) Wormpep data set: ---------------------------- There are 20245 CDS in autoace, 24236 when counting 3991 alternate splice forms. The 24236 sequences contain 10,713,280 base pairs in total. Modified entries 49 Deleted entries 28 New entries 62 Reappeared entries 0 Net change +34 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 9868 (40.7%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 11615 (47.9%) Some, but not all exon bases are covered by transcript evidence Predicted 2753 (11.4%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB accessions 24100 (99.4%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 24100 (99.4%) Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis elegans entries with WormBase-approved Gene name 24191 GeneModel correction progress WS208 -> WS209 ----------------------------------------- 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 help@wormbase.org -===================================================================================- New Data: --------- This release includes the coding transcripts predicted from the RNA-Seq project in 14 different life-stages and strains by LaDeana Hillier and Bob Waterston: Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. <http://www.ncbi.nlm.nih.gov/pubmed/19181841?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=1> Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH. Genome Res. 2009 Apr;19(4):657-66. Epub 2009 Jan 30.PMID: 19181841 Genome sequence updates: ----------------------- New Fixes: ---------- Known Problems: --------------- Other Changes: -------------- Proposed Changes / Forthcoming Data: ------------------------------------- Model Changes: ------------------------------------ Added / modified tags to better classify pseudogenes. -===================================================================================- 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 _____________