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New release of WormBase WS200, Wormpep200 and Wormrna200 Tue Feb 24 12:51:18 GMT 2009

WS200 was built by Anthony


This directory includes: i) database.WS200.*.tar.gz - compressed data for new release ii) models.wrm.WS200 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS200-WS199.dbcomp - log file reporting difference from last release v) wormpep200.tar.gz - full Wormpep distribution corresponding to WS200 vi) wormrna200.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS200.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS200.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS200.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS200.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS200.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.WS200.gz - for each C. briggsae protein, lists Best blastp match to

                                    human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.

xiii) geneIDs.WS200.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS200.gz - Mappings between PCR products and overlapping Genes

Release notes on the web:

Genome sequence composition:

      	WS200       	WS199      	change

a 32367419 32367419 +0 c 17780761 17780761 +0 g 17756942 17756942 +0 t 32367086 32367086 +0 n 0 0 +0 - 0 0 +0

Total 100272208 100272208 +0

Chromosomal Changes:

There are no changes to the chromosome sequences in this release.

Gene data set (Live C.elegans genes 39868)

Molecular_info 35554 (89.2%) Concise_description 5545 (13.9%) Reference 13406 (33.6%) WormBase_approved Gene name 25733 (64.5%) RNAi_result 22045 (55.3%) Microarray_results 20717 (52%) SAGE_transcript 18841 (47.3%)

Wormpep data set:

There are 20168 CDS in autoace, 23973 when counting 3805 alternate splice forms.

The 23973 sequences contain 10,580,574 base pairs in total.

Modified entries 28 Deleted entries 17 New entries 17 Reappeared entries 0

Net change +0

Status of entries: Confidence level of prediction (based on the amount of transcript evidence)

Confirmed 8704 (36.3%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 11719 (48.9%) Some, but not all exon bases are covered by transcript evidence Predicted 3550 (14.8%) No transcriptional evidence at all

Status of entries: Protein Accessions

UniProtKB accessions 23852 (99.5%)

Status of entries: Protein_ID's in EMBL

Protein_id 23852 (99.5%)

Gene <-> CDS,Transcript,Pseudogene connections

Caenorhabditis elegans entries with WormBase-approved Gene name 21468

Synchronisation with GenBank / EMBL:

No synchronisation issues

There are no gaps remaining in the genome sequence

For more info mail -===================================================================================-

New Data:

This archival release includes a new C. japonica assembly and associated set of gene predictions based on the methods determined by the nGASP project.

The C. brenneri gene set has been significantly improved through a manual curation effort.

Genome sequence updates:


New Fixes:

Known Problems:

We have discovered a long standing problem with the parsing of the blat outputs where sequences from other species are aligned to a genome. Only a small fraction of hits are affected but this does result in some odd alignments of ESTs to gaps in the contig based assemblies (which is what brought this to light). The alignments of transcripts to the their genome of origin is NOT affected.

We are working to fix this asap but in the mean time if you are interested in any cross species alignments of transcript data in WormBase that look odd please double check them with the BLAT server provided at UCSC ( )

Other Changes:

Proposed Changes / Forthcoming Data:

Model Changes:

None made


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.

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