Difference between revisions of "WS192"
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Latest revision as of 10:43, 21 December 2011
New release of WormBase WS192, Wormpep192 and Wormrna192 Tue Jun 24 11:23:32 BST 2008 WS192 was built by Gary Williams ====================================================================== This directory includes: i) database.WS192.*.tar.gz - compressed data for new release ii) models.wrm.WS192 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS192-WS191.dbcomp - log file reporting difference from last release v) wormpep192.tar.gz - full Wormpep distribution corresponding to WS192 vi) wormrna192.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS192.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS192.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS192.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS192.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS192.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.WS192.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS192.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS192.gz - Mappings between PCR products and overlapping Genes Release notes on the web: ------------------------- [[../../../../index.php/Release_notes|http://www.wormbase.org/wiki/index.php/Release_notes]] Genome sequence composition: ---------------------------- WS192 WS191 change ---------------------------------------------- a 32365950 32365950 +0 c 17779890 17779890 +0 g 17756040 17756040 +0 t 32365752 32365752 +0 n 0 0 +0 - 0 0 +0 Total 100267632 100267632 +0 Chromosomal Changes: -------------------- There are no changes to the chromosome sequences in this release. Gene data set (Live C.elegans genes 29849) ------------------------------------------ Molecular_info 28134 (94.3%) Concise_description 5386 (18%) Reference 7783 (26.1%) WormBase_approved Gene name 15410 (51.6%) RNAi_result 20812 (69.7%) Microarray_results 20456 (68.5%) SAGE_transcript 18838 (63.1%) Wormpep data set: ---------------------------- There are 20193 CDS in autoace, 23814 when counting 3621 alternate splice forms. The 23814 sequences contain 10,473,024 base pairs in total. Modified entries 66 Deleted entries 26 New entries 56 Reappeared entries 0 Net change +30 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 8451 (35.5%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 10973 (46.1%) Some, but not all exon bases are covered by transcript evidence Predicted 4390 (18.4%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB accessions 23675 (99.4%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 23675 (99.4%) Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis elegans entries with WormBase-approved Gene name 13744 GeneModel correction progress WS191 -> WS192 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 32 | -10 | St Louis | 152 | -22 | +---------+--------+ Members of known repeat families that overlap predicted exons; +---------+--------+ | Repeats | Change | +---------+--------+ Cambridge | 6 | 0 | St Louis | 6 | 0 | +---------+--------+ Synchronisation with GenBank / EMBL: ------------------------------------ No synchronisation issues There are no gaps remaining in the genome sequence --------------- For more info mail [mailto:help@wormbase.org help@wormbase.org] -===================================================================================- New Data: --------- Over 8000 new Mos transposon insertion alleles from the NemaGENETAG project have been added. Updates were made to the following database used for BLAST searches: Flybase IPI_human Yeast Genome sequence updates: ----------------------- None. New Fixes: ---------- None. Known Problems: --------------- None. Other Changes: -------------- None. Proposed Changes / Forthcoming Data: ------------------------------------- The website at [ftp://ftp.sanger.ac.uk/pub2/wormbase/WS192/genomes/ ftp://ftp.sanger.ac.uk/pub2/wormbase/WS192/genomes/] has been reorganised to contain information from several nematode species. These will be populated with data in the future as more information becomes available. corrected typo in the ?Antibody Model Model Changes: ------------------------------------ Slight restructure of ?Antibody class Well defined antibodies will be full populated with Isolation data. Ambigous anibodies will be connected to what it is believed to be by the Possible_pseudonym(_of) pair of tags No connection to CDS is required - just Gene is fine -===================================================================================- 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 [http://www.acedb.org/ 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.