WS204
New release of WormBase WS204, Wormpep204 and Wormrna204 Fri Jun 26 20:17:06 BST 2009
WS204 was built by Anthony
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This directory includes: i) database.WS204.*.tar.gz - compressed data for new release ii) models.wrm.WS204 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS204-WS203.dbcomp - log file reporting difference from last release v) wormpep204.tar.gz - full Wormpep distribution corresponding to WS204 vi) wormrna204.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS204.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS204.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS204.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS204.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS204.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.WS204.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS204.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS204.gz - Mappings between PCR products and overlapping Genes
Release notes on the web:
http://www.wormbase.org/wiki/index.php/Release_Schedule
Genome sequence composition:
WS204 WS203 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
Chromosomal Changes:
There are no changes to the chromosome sequences in this release.
Gene data set (Live C.elegans genes 39921)
Molecular_info 38212 (95.7%) Concise_description 5593 (14%) Reference 13459 (33.7%) WormBase_approved Gene name 25804 (64.6%) RNAi_result 22793 (57.1%) Microarray_results 21046 (52.7%) SAGE_transcript 19008 (47.6%)
Wormpep data set:
There are 20184 CDS in autoace, 24052 when counting 3868 alternate splice forms.
The 24052 sequences contain 10,630,049 base pairs in total.
Modified entries 49 Deleted entries 13 New entries 33 Reappeared entries 2
Net change +22
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
Confirmed 9759 (40.6%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 11506 (47.8%) Some, but not all exon bases are covered by transcript evidence Predicted 2787 (11.6%) No transcriptional evidence at all
Status of entries: Protein Accessions
UniProtKB accessions 23915 (99.4%)
Status of entries: Protein_ID's in EMBL
Protein_id 23915 (99.4%)
Gene <-> CDS,Transcript,Pseudogene connections
Caenorhabditis elegans entries with WormBase-approved Gene name 24143
GeneModel correction progress WS203 -> WS204
Confirmed introns not in a CDS gene model;
+---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 0 | 0 | St Louis | 0 | 0 | +---------+--------+
Members of known repeat families that overlap predicted exons;
+---------+--------+ | Repeats | Change | +---------+--------+ Cambridge | 0 | 0 | St Louis | 0 | 0 | +---------+--------+
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:
This release includes the first inclusion in WormBase of the M. hapla genome.
Genome sequence updates:
New Fixes:
Known Problems:
Other Changes:
Proposed Changes / Forthcoming Data:
The M.incognita genome will be included soon - maybe as a post release addition to this one!
Model Changes:
Fixed Transposon white space issues.
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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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