New release of WormBase WS208, Wormpep208 and Wormrna208 Tue Oct 27 13:31:22 GMT 2009
WS208 was built by Anthony
This directory includes: i) database.WS208.*.tar.gz - compressed data for new release ii) models.wrm.WS208 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS208-WS207.dbcomp - log file reporting difference from last release v) wormpep208.tar.gz - full Wormpep distribution corresponding to WS208 vi) wormrna208.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS208.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS208.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS208.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS208.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS208.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.WS208.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS208.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS208.gz - Mappings between PCR products and overlapping Genes
Release notes on the web:
Genome sequence composition:
WS208 WS207 change
a 32367418 32367418 +0 c 17780763 17780763 +0 g 17756943 17756943 +0 t 32367086 32367086 +0 n 0 0 +0 - 0 0 +0
Total 100272210 100272210 +0
There are no changes to the chromosome sequences in this release.
Gene data set (Live C.elegans genes 39999)
Molecular_info 38295 (95.7%) Concise_description 5605 (14%) Reference 13653 (34.1%) WormBase_approved Gene name 25843 (64.6%) RNAi_result 22833 (57.1%) Microarray_results 21058 (52.6%) SAGE_transcript 19056 (47.6%)
Wormpep data set:
There are 20238 CDS in autoace, 24202 when counting 3964 alternate splice forms.
The 24202 sequences contain 10,693,111 base pairs in total.
Modified entries 13 Deleted entries 12 New entries 29 Reappeared entries 0
Net change +17
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
Confirmed 9843 (40.7%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 11605 (48.0%) Some, but not all exon bases are covered by transcript evidence Predicted 2754 (11.4%) No transcriptional evidence at all
Status of entries: Protein Accessions
UniProtKB accessions 24062 (99.4%)
Status of entries: Protein_ID's in EMBL
Protein_id 24062 (99.4%)
Gene <-> CDS,Transcript,Pseudogene connections
Caenorhabditis elegans entries with WormBase-approved Gene name 24187
Synchronisation with GenBank / EMBL:
No synchronisation issues
There are no gaps remaining in the genome sequence
For more info mail firstname.lastname@example.org -===================================================================================-
H.contortus included in orthology determination.
Genome sequence updates:
Some abherrant gene names have been removed.
Proposed Changes / Forthcoming Data:
added Title to ?Analysis
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.
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