Difference between revisions of "WS186"
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Revision as of 05:00, 7 January 2008
Release Notes
New release of WormBase WS186, Wormpep186 and Wormrna186 Fri Dec 21 08:57:59 GMT 2007 WS186 was built by Mary Ann ====================================================================== This directory includes: i) database.WS186.*.tar.gz - compressed data for new release ii) models.wrm.WS186 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS186-WS185.dbcomp - log file reporting difference from last release v) wormpep186.tar.gz - full Wormpep distribution corresponding to WS186 vi) wormrna186.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS186.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS186.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS186.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS186.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS186.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.WS186.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS186.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS186.gz - Mappings between PCR products and overlapping Genes Release notes on the web: ------------------------- http://www.wormbase.org/wiki/index.php/Release_notes Genome sequence composition: ---------------------------- WS186 WS185 change ---------------------------------------------- a 32365950 32365949 +1 c 17779886 17779887 -1 g 17756037 17756036 +1 t 32365750 32365750 +0 n 0 0 +0 - 0 0 +0 Total 100267623 100267622 +1 Chromosomal Changes: -------------------- Chromosome: II 8655100 8655100 1 -> 8655100 8655100 1 Chromosome: X 14718205 14718204 0 -> 14718205 14718205 1 Gene data set (Live C.elegans genes 29624) ------------------------------------------ Molecular_info 27922 (94.3%) Concise_description 5074 (17.1%) Reference 7523 (25.4%) WormBase_approved Gene name 15141 (51.1%) RNAi_result 20733 (70%) Microarray_results 19959 (67.4%) SAGE_transcript 18722 (63.2%) Wormpep data set: ---------------------------- There are 20169 CDS in autoace, 23645 when counting 3476 alternate splice forms. The 23645 sequences contain base pairs in total. Modified entries 83 Deleted entries 30 New entries 48 Reappeared entries 3 Net change +21 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 8316 (35.2%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 10966 (46.4%) Some, but not all exon bases are covered by transcript evidence Predicted 4363 (18.5%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB/Swiss-Prot accessions 3644 (15.4%) UniProtKB/TrEMBL accessions 19604 (82.9%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 23248 (98.3%) Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis elegans entries with WormBase-approved Gene name 13490 GeneModel correction progress WS185 -> WS186 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 124 | 65 | St Louis | 472 | 27 | +---------+--------+ 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 worm@sanger.ac.uk -===================================================================================- New Data: --------- Genome sequence updates: ----------------------- F33C8 insertion catgctaagccaattctcatcggccggagGtccaacacctctatccatcgaaccgtgtag D2085 deletion cactttcagaatcgctgaagcatttaatgtcaCcggacctttcaatatgcagctcattgctaaaaataacga D2085 insertion cactttcagaatcgctgaagcatttaatgtcaAcggacctttcaatatgcagctcattgctaaaaataacga New Fixes: ---------- Known Problems: --------------- Other Changes: -------------- Proposed Changes / Forthcoming Data: ------------------------------------- Model Changes: ------------------------------------ Removed the Microarray_results tag from the ?Microarray class and consequently the XREF between ?Microarray_results and ?Microarray classes. ?Microarray_results class will still have a link to ?Microarray. The reason for that is that AceDB begins to struggle when one object is linked to very many, which is the case for some (notably tiling) arrays. -===================================================================================- 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.