Difference between revisions of "WS170"
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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 |
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Latest revision as of 10:51, 21 December 2011
Release Notes
New release of WormBase WS170, Wormpep170 and Wormrna170 Fri Jan 19 09:31:14 GMT 2007 WS170 was built by Paul Davis ====================================================================== This directory includes: i) database.WS170.*.tar.gz - compressed data for new release ii) models.wrm.WS170 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS170-WS169.dbcomp - log file reporting difference from last release v) wormpep170.tar.gz - full Wormpep distribution corresponding to WS170 vi) wormrna170.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS170.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS170.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS170.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS170.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS170.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.WS170.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS170.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS170.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: ---------------------------- WS170 WS169 change ---------------------------------------------- a 32365889 32365889 +0 c 17779856 17779856 +0 g 17756016 17756016 +0 t 32365689 32365689 +0 n 0 0 +0 Total 100267450 100267450 +0 Chromosomal Changes: -------------------- There are no changes to the chromosome sequences in this release. Gene data set (Live C.elegans genes 23977) ------------------------------------------ Molecular_info 22281 (92.9%) Concise_description 4380 (18.3%) Reference 6708 (28%) CGC_approved Gene name 8940 (37.3%) RNAi_result 19842 (82.8%) Microarray_results 19134 (79.8%) SAGE_transcript 20020 (83.5%) Wormpep data set: ---------------------------- There are 20082 CDS in autoace, 23224 when counting 3142 alternate splice forms. The 23224 sequences contain 10,186,194 base pairs in total. Modified entries 24 Deleted entries 13 New entries 16 Reappeared entries 0 Net change +3 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 7825 (33.7%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 10746 (46.3%) Some, but not all exon bases are covered by transcript evidence Predicted 4653 (20.0%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB/Swiss-Prot accessions 3269 (14.1%) UniProtKB/TrEMBL accessions 19437 (83.7%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 22706 (97.8%) Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved) --------------------------------------------- Entries with CGC-approved Gene name 7298 GeneModel correction progress WS169 -> WS170 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 15 | 0 | St Louis | 10 | -1 | +---------+--------+ 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 help@wormbase.org -===================================================================================- New Data: --------- 1) If you are planning to run mass spectrometry experiments, you might like to search the file of translated open reading frames in: ftp://ftp.sanger.ac.uk/pub/wormbase/data/translated_orfs.WS170.gz in addition to the set of curated wormpep proteins. If you have questions about submitting any types of data to wormbase, please contact: submit@wormbase.org" Genome sequence updates: ----------------------- New Fixes: ---------- Known Problems: --------------- 16 elegans peptides failed to run through the blastp pipeline. Other Changes: -------------- Proposed Changes / Forthcoming Data: ------------------------------------- Model Changes: ------------------------------------ PaulD Added tag to ?Operon to track removed operons and #Evidence to the Remark. ?Operon History Deprecated Text #Evidence Remark Text #Evidence further operon related addition. ?Trans_splice_leader . Inferred #Evidence ========================================================================================================== MichealH Removed the erroneous UNIQUE from the Ortholog_other tag added last time. It is actually not needed at all. ?Gene Ortholog_other  ?Database ?Database_field ?Accession_number ?Species #Evidence ========================================================================================================== GaryW Corrected type in Protein class introduced last time ?Protein Contains_peptide ?Mass_spec_peptonide <---- ========================================================================================================== Igor/Raymond ?Expression_cluster and ?Anatomy_term changes to describe microarray experiments involving expression profiling in a particular tissue or cell. ?Expression_cluster Anatomy_term ?Anatomy_term XREF Expression_cluster #Evidence ?Anatomy_term Attribute_of Expression_cluster ?Expression_cluster XREF Anatomy_term #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. ____________ END _____________