Difference between revisions of "WS216"
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There are no gaps remaining in the genome sequence | There are no gaps remaining in the genome sequence | ||
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− | For more info mail | + | For more info mail help@wormbase.org |
-===================================================================================- | -===================================================================================- | ||
Latest revision as of 11:10, 21 December 2011
Release Letter
New release of WormBase WS216, Wormpep216 and Wormrna216 Tue Jun 29 12:53:35 BST 2010 WS216 was built by [Michael Paulini] ====================================================================== This directory includes: i) database.WS216.*.tar.gz - compressed data for new release ii) models.wrm.WS216 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS216-WS215.dbcomp - log file reporting difference from last release v) wormpep216.tar.gz - full Wormpep distribution corresponding to WS216 vi) wormrna216.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS216.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS216.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS216.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS216.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS216.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.WS216.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS216.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS216.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: ---------------------------- WS216 WS215 change ---------------------------------------------- a 32367418 32367418 +0 c 17780787 17780787 +0 g 17756985 17756985 +0 t 32367086 32367086 +0 n 0 0 +0 - 0 0 +0 Total 100272276 100272276 +0 Chromosomal Changes: -------------------- There are no changes to the chromosome sequences in this release. Gene data set (Live C.elegans genes 40162) ------------------------------------------ Molecular_info 38477 (95.8%) Concise_description 5666 (14.1%) Reference 14028 (34.9%) WormBase_approved Gene name 25983 (64.7%) RNAi_result 22924 (57.1%) Microarray_results 21070 (52.5%) SAGE_transcript 19141 (47.7%) Wormpep data set: ---------------------------- There are 20364 CDS in autoace, 24652 when counting 4288 alternate splice forms. The 24652 sequences contain 10,865,930 base pairs in total. Modified entries 23 Deleted entries 26 New entries 79 Reappeared entries 3 Net change +56 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 10131 (41.1%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 11781 (47.8%) Some, but not all exon bases are covered by transcript evidence Predicted 2740 (11.1%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB accessions 24474 (99.3%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 24475 (99.3%) Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis elegans entries with WormBase-approved Gene name 24346 GeneModel correction progress WS215 -> WS216 ----------------------------------------- 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: ------------------------------------ CHROMOSOME_I sequence AC024794 CHROMOSOME_I sequence AF067219 CHROMOSOME_II sequence AF025454 CHROMOSOME_II sequence U49955 CHROMOSOME_II sequence U23519 CHROMOSOME_II sequence U41278 CHROMOSOME_II sequence U29244 CHROMOSOME_II sequence U39999 CHROMOSOME_III sequence U00057 CHROMOSOME_III sequence U23514 CHROMOSOME_III sequence U50193 CHROMOSOME_III sequence U23177 CHROMOSOME_III sequence AC006679 CHROMOSOME_III sequence L16621 CHROMOSOME_IV sequence AF038604 CHROMOSOME_IV sequence U97593 CHROMOSOME_V sequence AF024503 CHROMOSOME_X sequence U41553 CHROMOSOME_X sequence U39653 CHROMOSOME_X sequence U64859 CHROMOSOME_X sequence U39741 CHROMOSOME_X sequence AC199239 There are no gaps remaining in the genome sequence --------------- For more info mail help@wormbase.org -===================================================================================- New Data: --------- * new Pristionchus gene curation: changes to 17 genes used in Pristionchus publications * Brugia gene set refinement: further gene merges and isoform cleanups Genome sequence updates: ----------------------- New Fixes: ---------- Known Problems: --------------- * three C.remanei CDSes don't have gene ids Other Changes: -------------- Proposed Changes / Forthcoming Data: ------------------------------------- * added Brief_id to ?Position_Matrix class * new ?Molecule class 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 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 _____________
known bugs
confirmed introns
There seems to be a systematic 12bp shift in the confirmed intron features coming from RNAseq data - Removed for WS217
None of the Transcript confirmed intron data was processed for this build. - Resolved for WS217
missing C.remanei genes
There are three C.remanei CDSes that are missing gene ids
AGP
there are errors in the C.elegans AGP file (clones being out of sync with the public repositories), which will be solved in WS217.