Difference between revisions of "WS190"
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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 16:46, 21 December 2011
Contents
Release Notes
New release of WormBase WS190, Wormpep190 and Wormrna190 Fri Apr 25 11:03:36 BST 2008 WS190 was built by Anthony ====================================================================== This directory includes: i) database.WS190.*.tar.gz - compressed data for new release ii) models.wrm.WS190 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS190-WS189.dbcomp - log file reporting difference from last release v) wormpep190.tar.gz - full Wormpep distribution corresponding to WS190 vi) wormrna190.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS190.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS190.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS190.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS190.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS190.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.WS190.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS190.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS190.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: ---------------------------- WS190 WS189 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 29802) ------------------------------------------ Molecular_info 28107 (94.3%) Concise_description 5308 (17.8%) Reference 7700 (25.8%) WormBase_approved Gene name 15262 (51.2%) RNAi_result 20797 (69.8%) Microarray_results 20462 (68.7%) SAGE_transcript 18839 (63.2%) Wormpep data set: ---------------------------- There are 20177 CDS in autoace, 23771 when counting 3594 alternate splice forms. The sequences contain 10,449,259 base pairs in total. Modified entries 71 Deleted entries 27 New entries 68 Reappeared entries 0 Net change +41 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 8418 (35.4%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 10964 (46.1%) Some, but not all exon bases are covered by transcript evidence Predicted 4389 (18.5%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB accessions 23622 (99.4%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 23625 (99.4%) Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis elegans entries with WormBase-approved Gene name 13617 GeneModel correction progress WS189 -> WS190 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 57 | -9 | St Louis | 165 | 46 | +---------+--------+ Members of known repeat families that overlap predicted exons; +---------+--------+ | Repeats | Change | +---------+--------+ Cambridge | 6 | 1 | St Louis | 6 | 1 | +---------+--------+ Synchronisation with GenBank / EMBL: ------------------------------------ CHROMOSOME_II sequence U40030 There are no gaps remaining in the genome sequence --------------- For more info mail help@wormbase.org -===================================================================================- New Data: --------- Uniprot databases update to Knowledgebase major release 13. This now includes Brugia malayi proteins. IPI_human blast database has been updated. All blast and transcript alignments have been update for C.briggsae and C.remanei Genome sequence updates: ----------------------- New Fixes: ---------- Known Problems: --------------- The automated coding_transcript building code does not currently work with C.remanei so these CDSs do not have UTRs Other Changes: -------------- The methods for running blastx have changed slightly due to updating to the latest version of the Ensembl schema/code. Rather than using the sequenced cosmids as units of sequence to blast against, sequencial 75kb chunks are used. This has meant we have had to add the parameter hspsepsmax=7500. see http://blast.wustl.edu/blast/parameters.html#hspsepsmax for details. Proposed Changes / Forthcoming Data: ------------------------------------- Model Changes: ------------------------------------ Added tags to ?Feature to connect to ?Operon, ?Gene_regulation and ?Expr_pattern Connected ?Rearrangement to ?Phenotype Changed Phenotype to Legacy_information in ?Gene to avoid confussion Updates to ?Neurodata and ?Neuro_location -===================================================================================- 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 _____________
Patches
Molecular Changes Patches
- some missense/nonsense molecular changes were wrong. patch files are available from Sanger (apply in order):
Twinscan Prediction Patch
The coordinates of the Twinscan predictions were wrong. A patch can be picked up from Sanger at: Twinscan Patch
additional low complexity features
I created additional RepeatMasker low-complexity features (per user feedback) which are available as:
- ACE-file
- GFF2-files (tarballed)