WS191
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Release Notes
New release of WormBase WS191, Wormpep191 and Wormrna191 Mon Jun 2 09:50:52 BST 2008 WS191 was built by Mary Ann Tuli ====================================================================== This directory includes: i) database.WS191.*.tar.gz - compressed data for new release ii) models.wrm.WS191 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS191-WS190.dbcomp - log file reporting difference from last release v) wormpep191.tar.gz - full Wormpep distribution corresponding to WS191 vi) wormrna191.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS191.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS191.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS191.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS191.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS191.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.WS191.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS191.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS191.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: ---------------------------- WS191 WS190 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 29821) ------------------------------------------ Molecular_info 28126 (94.3%) Concise_description 5374 (18%) Reference 7725 (25.9%) WormBase_approved Gene name 15353 (51.5%) RNAi_result 20808 (69.8%) Microarray_results 20461 (68.6%) SAGE_transcript 18840 (63.2%) Wormpep data set: ---------------------------- There are 20195 CDS in autoace, 23784 when counting 3589 alternate splice forms. The 23784 sequences contain 10,458,215 base pairs in total. Modified entries 27 Deleted entries 19 New entries 31 Reappeared entries 0 Net change +12 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 8431 (35.4%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 10965 (46.1%) Some, but not all exon bases are covered by transcript evidence Predicted 4388 (18.4%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB accessions 23640 (99.4%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 23644 (99.4%) Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis elegans entries with WormBase-approved Gene name 13707 GeneModel correction progress WS190 -> WS191 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 42 | -15 | St Louis | 174 | 9 | +---------+--------+ Members of known repeat families that overlap predicted exons; +---------+--------+ | Repeats | Change | +---------+--------+ Cambridge | 6 | 0 | St Louis | 6 | 0 | +---------+--------+ Synchronisation with GenBank / EMBL: ------------------------------------ CHROMOSOME_II sequence U40030 There are no gaps remaining in the genome sequence --------------- For more info mail [mailto:worm@sanger.ac.uk worm@sanger.ac.uk] -===================================================================================- New Data: --------- Blast database versions: - yeast29.pep Proposed Changes / Forthcoming Data: ------------------------------------- nGASP gene predictions are beginning to be displayed through WormBase. Genome browser views are already available for final elegans and briggsae predictions and component gene predictions for brenneri, japonica remanei and B. malayi. These will be updated once final predictions are available. Full integration, including orthologue determination and naming along with the presentation of gene pages etc will will occur over the forthcoming releases. Model Changes: ------------------------------------ Added tags to connect CGH deletions that may hit genes. ?Variation.Possibly_affects ?Gene XREF Possibly_affected_by #Evidence ?Gene.Possibly_affected_by ?Variation XREF Possibly_affects #Evidence Added score type tags to Interaction_info #Interaction_info Confidence Confidence_level UNIQUE Float P_value -===================================================================================- 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. ____________ END _____________
Patches
- Missing TreeFam ids
I told Norie and Todd already to load it.