New release of WormBase WS207, Wormpep207 and Wormrna207 Mon Sep 28 11:47:26 BST 2009
WS207 was built by Paul Davis
This directory includes: i) database.WS207.*.tar.gz - compressed data for new release ii) models.wrm.WS207 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS207-WS206.dbcomp - log file reporting difference from last release v) wormpep207.tar.gz - full Wormpep distribution corresponding to WS207 vi) wormrna207.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS207.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS207.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS207.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS207.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS207.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.WS207.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS207.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS207.gz - Mappings between PCR products and overlapping Genes
Release notes on the web:
Genome sequence composition:
WS207 WS206 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 39985)
Molecular_info 38279 (95.7%) Concise_description 4925 (12.3%) Reference 13643 (34.1%) WormBase_approved Gene name 25839 (64.6%) RNAi_result 22830 (57.1%) Microarray_results 21055 (52.7%) SAGE_transcript 19046 (47.6%)
Wormpep data set:
There are 20231 CDS in autoace, 24185 when counting 3954 alternate splice forms.
The 24185 sequences contain 10,689,789 base pairs in total.
Modified entries 146 Deleted entries 25 New entries 67 Reappeared entries 3
Net change +45 The differnce between the total CDS's of this (24185) and the last build (24143) does not equal the net change 45 Please investigate! !
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
Confirmed 9819 (40.6%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 11573 (47.9%) Some, but not all exon bases are covered by transcript evidence Predicted 2793 (11.5%) No transcriptional evidence at all
Status of entries: Protein Accessions
UniProtKB accessions 24045 (99.4%)
Status of entries: Protein_ID's in EMBL
Protein_id 24045 (99.4%)
Gene <-> CDS,Transcript,Pseudogene connections
Caenorhabditis elegans entries with WormBase-approved Gene name 24181
Synchronisation with GenBank / EMBL:
No synchronisation issues
There are no gaps remaining in the genome sequence
For more info mail firstname.lastname@example.org -===================================================================================-
Duplicon region features from paper WBPaper00034747 http://www.wormbase.org/db/misc/paper?name=WBPaper00034747;class=Paper WBsf038821 - WBsf042304
HTZ-1 binding site regions added WBPaper00032180 http://www.wormbase.org/db/misc/paper?name=WBPaper00032180;class=Paper WBsf042314 - WBsf047477
Genome sequence updates:
Longtext EST/mRNA patched
70,000 Sequence entries were missing their EMBL/GENBANK accession info inm previous releases.
Proposed Changes / Forthcoming Data:
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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