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new release of WormBase WS176, Wormpep176 and Wormrna176 Mon May 21 11:58:06 BST 2007 WS176 was built by Mary Ann Tuli ====================================================================== This directory includes: i) database.WS176.*.tar.gz - compressed data for new release ii) models.wrm.WS176 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS176-WS175.dbcomp - log file reporting difference from last release v) wormpep176.tar.gz - full Wormpep distribution corresponding to WS176 vi) wormrna176.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS176.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS176.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS176.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS176.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS176.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.WS176.gz - for each C. briggsae protein, lists Best blastp match to human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins. xiii) geneIDs.WS176.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS176.gz - Mappings between PCR products and overlapping Genes Release notes on the web: ------------------------- Genome sequence composition: ---------------------------- WS175 WS174 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 24101) ------------------------------------------ Molecular_info 22410 (93%) Concise_description 4578 (19%) Reference 7003 (29.1%) CGC_approved Gene name 9213 (38.2%) RNAi_result 19876 (82.5%) Microarray_results 19152 (79.5%) SAGE_transcript 20034 (83.1%) Wormpep data set: ---------------------------- There are 20131 CDS in autoace, 23375 when counting 3244 alternate splice forms. The 23375 sequences contain 10,266,608 base pairs in total. Modified entries 91 Deleted entries 77 New entries 175 Reappeared entries 4 Net change +102 Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 7940 (34.0%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 10811 (46.3%) Some, but not all exon bases are covered by transcript evidence Predicted 4624 (19.8%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB/Swiss-Prot accessions 3523 (15.1%) UniProtKB/TrEMBL accessions 19412 (83.0%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 22935 (98.1%) Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved) --------------------------------------------- Entries with CGC-approved Gene name 7573 GeneModel correction progress WS175 -> WS176 ----------------------------------------- Confirmed introns not in a CDS gene model; +---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 70 | -103 | St Louis | 179 | -33 | +---------+--------+ 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 -===================================================================================- New Data: --------- A set of 51,623 mass spectroscopy peptides from Gennifer Merrihew at Michael MacCoss's laboratory has been added to this release. Proteins have been fragmented and the molecular weights of the fragments have then been used to deduce the sequence of the fragments by comparing to a database of C. elegans protein sequences. The peptides were mapped to the genome using the known positions of the peptides in the matching proteins and the known positions of the proteins' genes on the genome. This data gives confirmatory evidence of many exons and (where they span splice sites) some introns. Genome sequence updates: ----------------------- None New Fixes: ---------- None Known Problems: --------------- None Other Changes: -------------- None Proposed Changes / Forthcoming Data: ------------------------------------- A number of genomic canonical clones are going to be updated for WS177. F54F7 deletion tagctcaccagcttgcacgGgaagtgaaagtcttgaaata F28H7 deletion aacaaaatcttgcaactagTaatgtgaaaaagtgtggact K07A1 insertion ttctcaaatttcagtttatTggaacattacaaatatgtgt F13G3 insertion tttttttcagacaccgttcgtttggctccgGcgcgatcaacatggtgatggttgcacaagg R10E11 deletion gccacctggaaatcaatcagctcctcaaaaAgaattccgaatctgcctatattctgttcta 07A1 insertion ttctcaaatttcagtttatTggaacattacaaatatgtgt F13G3 insertion tttttttcagacaccgttcgtttggctccgGcgcgatcaacatggtgatggttgcacaagg R10E11 deletion gccacctggaaatcaatcagctcctcaaaaAgaattccgaatctgcctatattctgttcta K11H3 insertion gcattaacaacacacggaaatcgaaatggaCcacttcgttatagtcttcttcaacaacgag F13G3 insertion ccttgtgcaaccatcaccatgttgatcgcgGcggagccaaacgaacggtgtctgaaaaaaa Y95D11A shift-overlap with F49D11 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 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 _____________