Difference between revisions of "WS188"
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== Inparanoid 6 human orthologs == | == Inparanoid 6 human orthologs == | ||
− | + | For some Inparonoid 6 worm genes with human orthologs, a C.elegans gene is erroneously named as human ortholog. | |
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Revision as of 18:22, 13 March 2008
Contents
Release Notes
New release of WormBase WS188, Wormpep188 and Wormrna188 Fri Feb 29 14:53:33 GMT 2008 WS188 was built by [Michael Han (mh6@sanger.ac.uk)] ====================================================================== This directory includes: i) database.WS188.*.tar.gz - compressed data for new release ii) models.wrm.WS188 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS188-WS187.dbcomp - log file reporting difference from last release v) wormpep188.tar.gz - full Wormpep distribution corresponding to WS188 vi) wormrna188.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS188.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS188.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS188.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS188.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS188.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.WS188.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS188.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS188.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: ---------------------------- WS188 WS187 change ---------------------------------------------- a 32365950 32365950 +0 c 17779886 17779886 +0 g 17756037 17756037 +0 t 32365750 32365750 +0 n 0 0 +0 - 0 0 +0 Total 100267623 100267623 +0 Chromosomal Changes: -------------------- There are no changes to the chromosome sequences in this release. Gene data set (Live C.elegans genes 29684) ------------------------------------------ Molecular_info 27983 (94.3%) Concise_description 5203 (17.5%) Reference 7620 (25.7%) WormBase_approved Gene name 15215 (51.3%) RNAi_result 20749 (69.9%) Microarray_results 19972 (67.3%) SAGE_transcript 18766 (63.2%) Wormpep data set: ---------------------------- There are 20178 CDS in autoace, 23693 when counting 3515 alternate splice forms. The 23693 sequences contain base pairs in total. Modified entries 132 Deleted entries 27 New entries 55 Reappeared entries 3 Net change +31 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 8370 (35.3%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 10956 (46.2%) Some, but not all exon bases are covered by transcript evidence Predicted 4367 (18.4%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB/Swiss-Prot accessions 3676 (15.5%) UniProtKB/TrEMBL accessions 19679 (83.1%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 23355 (98.6%) Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis elegans entries with WormBase-approved Gene name 13564 GeneModel correction progress WS187 -> WS188 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 0 | -127 | St Louis | 0 | -404 | +---------+--------+ Members of known repeat families that overlap predicted exons; +---------+--------+ | Repeats | Change | +---------+--------+ Cambridge | 0 | -6 | St Louis | 0 | -6 | +---------+--------+ 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: --------- * updated C.briggsae genes / transcripts and BLAT alignments * included new ESTs from WashU * ~2500 new C.brenneri ESTs * ~1600 new C.japonica ESTs * added OMIM tags to ortholog H.sapiens genes * added Inparanoid 6 data for C.elegans <-> H.sapiens orthologs Genome sequence updates: ----------------------- none New Fixes: ---------- Known Problems: --------------- Affymetrix / Agilent / GSC probe flatfiles will be made available at a later date. Other Changes: -------------- Proposed Changes / Forthcoming Data: ------------------------------------- changes to the CGH array alleles, to store gap between internal and external deletion points Model Changes: ------------------------------------ new Evidence type Variation_evidence -===================================================================================- 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.
Fixes/Patches
microarray_probe tables
the missing files were released on 3rd of March 2008 at:
- ftp://ftp.sanger.ac.uk/pub2/wormbase/WS188/affy_oligo_mapping.gz
- ftp://ftp.sanger.ac.uk/pub2/wormbase/WS188/agil_oligo_mapping.gz
- ftp://ftp.sanger.ac.uk/pub2/wormbase/WS188/gsc_oligo_mapping.gz
Inparanoid 6 human orthologs
For some Inparonoid 6 worm genes with human orthologs, a C.elegans gene is erroneously named as human ortholog.