https://wiki.wormbase.org/index.php?title=WS228&feed=atom&action=history
WS228 - Revision history
2024-03-29T01:59:54Z
Revision history for this page on the wiki
MediaWiki 1.33.0
https://wiki.wormbase.org/index.php?title=WS228&diff=12776&oldid=prev
Mh6: WS228 patch
2011-11-11T10:37:38Z
<p>WS228 patch</p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 10:37, 11 November 2011</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Bug Fixes ===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Bug Fixes ===</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">==== eggNOG ====</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">missing eggNOG data can be found here: ftp://ftp.sanger.ac.uk/pub2/wormbase/releases/WS228/patches/eggNOG.ace</ins></div></td></tr>
</table>
Mh6
https://wiki.wormbase.org/index.php?title=WS228&diff=12582&oldid=prev
Pdavis: /* Release Notes */
2011-09-30T13:54:18Z
<p><span dir="auto"><span class="autocomment">Release Notes</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 13:54, 30 September 2011</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Variation_data - </div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Variation_data - <ins class="diffchange diffchange-inline"> Over 65,000 variations identified by the</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">Itai Yanai lab and published in PMID 21367940 Genome Res.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">2011 Core promoter T-blocks correlate with gene expression levels in C.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">elegans. Hryshkevich U, Hashimshony T, Yanai I. were added to this release. </ins></div></td></tr>
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Pdavis
https://wiki.wormbase.org/index.php?title=WS228&diff=12581&oldid=prev
Pdavis: /* Release Notes */
2011-09-30T13:40:44Z
<p><span dir="auto"><span class="autocomment">Release Notes</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 13:40, 30 September 2011</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l403" >Line 403:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>http://wiki.wormbase.org/index.php/WS228_Models.wrm</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>http://wiki.wormbase.org/index.php/WS228_Models.wrm</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>For more info mail <del class="diffchange diffchange-inline">worm</del>@<del class="diffchange diffchange-inline">sanger</del>.<del class="diffchange diffchange-inline">ac.uk</del></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>For more info mail <ins class="diffchange diffchange-inline">hinxton</ins>@<ins class="diffchange diffchange-inline">wormbase</ins>.<ins class="diffchange diffchange-inline">org</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>-===================================================================================-</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>-===================================================================================-</div></td></tr>
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Pdavis
https://wiki.wormbase.org/index.php?title=WS228&diff=12580&oldid=prev
Pdavis: /* Release Notes */
2011-09-30T13:37:08Z
<p><span dir="auto"><span class="autocomment">Release Notes</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 13:37, 30 September 2011</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>------------------------------------</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>------------------------------------</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">WS228 models v 1.2</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">This cycle we see 5 model changes.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">#Homology type - COG - proposed by Michael</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">?CDS - Start_not_found <UNIQUE> int - proposed by Michael</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">?Transcript - u21RNA -> piRNA conversion - proposed by Gary</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> Has implications for StLouis sequence database.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">?Expression_cluster - proposed by Wen</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">?Variation - Readthrough Text #Evidence - Proposed by Kevin</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> & corresponding change in the #Molecular_change hash.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">More infromation and a human readable diff can be found here:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">http://wiki.wormbase.org/index.php/WS228_Models.wrm</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>For more info mail worm@sanger.ac.uk</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>For more info mail worm@sanger.ac.uk</div></td></tr>
</table>
Pdavis
https://wiki.wormbase.org/index.php?title=WS228&diff=12579&oldid=prev
Pdavis: Created page with '__TOC__ === Release Notes === <pre> New release of WormBase WS228 WS228 was built by Paul Davis -==============================================================================…'
2011-09-30T13:32:04Z
<p>Created page with '__TOC__ === Release Notes === <pre> New release of WormBase WS228 WS228 was built by Paul Davis -==============================================================================…'</p>
<p><b>New page</b></p><div>__TOC__<br />
<br />
=== Release Notes ===<br />
<br />
<pre><br />
New release of WormBase WS228<br />
<br />
WS228 was built by Paul Davis<br />
-===================================================================================-<br />
The WS228 build directory includes:<br />
species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:<br />
- G_SPECIES.WS228.genomic.fa.gz - Unmasked genomic DNA<br />
- G_SPECIES.WS228.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA<br />
- G_SPECIES.WS228.genomic_softmasked.fa.gz - Soft-masked (repeats lower-cased) genomic DNA<br />
- G_SPECIES.WS228.protein.fa.gz - Current live protein set<br />
- G_SPECIES.WS228.cds_transcripts.fa.gz - Spliced cDNA sequence for the CDS portion of protein-coding transcripts<br />
- G_SPECIES.WS228.ncrna_transcripts.fa.gz - Spliced cDNA sequence for non-coding RNA transcripts<br />
- G_SPECIES.WS228.intergenic_sequences.fa.gz - DNA sequence between pairs of adjacent genes<br />
- G_SPECIES.WS228.annotations.gff[2|3].gz - Sequence features in either GFF2 or GFF3 format<br />
- G_SPECIES.WS228.ests.fa.gz - ESTs and mRNA sequences extracted from the public databases<br />
- G_SPECIES.WS228.best_blastp_hits.txt.gz - Best blastp matches to human, fly, yeast, and non-WormBase Uniprot proteains<br />
- G_SPECIES.WS228.*pep_package.tar.gz - latest version of the [worm|brig|bren|rema|jap|ppa]pep package (if updated since last release)<br />
- annotation/ - contains additional annotations:<br />
- G_SPECIES.WS228.confirmed_genes.txt.gz - DNA sequences of all genes confirmed by EST &/or cDNA<br />
- G_SPECIES.WS228.cDNA2orf.txt.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)<br />
- G_SPECIES.WS228.geneIDs.txtgz - list of all current gene identifiers with CGC & molecular names (when known)<br />
- G_SPECIES.WS228.PCR_product2gene.txt.gz - Mappings between PCR products and overlapping Genes<br />
- G_SPECIES.WS228.*oligo_mapping.txt.gz - Oligo array mapping files<br />
- G_SPECIES.WS228.knockout_consortium_alleles.xml.gz - Table of Knockout Consortium alleles<br />
- G_SPECIES.WS228.SRA_gene_expression.tar.gz - Tables of gene expression values computed from SRA RNASeq data<br />
acedb DIR - Everything needed to generate a local copy of the The Primary database<br />
- database.WS228.*.tar.gz - compressed acedb database for new release<br />
- models.wrm.WS228 - the latest database schema (also in above database files)<br />
- WS228-WS227.dbcomp - log file reporting difference from last release<br />
- *Non_C_elegans_BLASTX/ - This directory contains the blastx data for non-elegans species<br />
(reduces the size of the main database)<br />
COMPARATIVE_ANALYSIS DIR - comparative analysis files<br />
- compara.WS228.tar.bz2 - gene-tree and alignment GFF files<br />
- wormpep_clw.WS228.sql.bz2 - ClustalW protein multiple alignments<br />
ONTOLOGY DIR - gene_associations, obo files for (phenotype GO anatomy) and associated association files<br />
<br />
<br />
Release notes on the web:<br />
-------------------------<br />
http://www.wormbase.org/wiki/index.php/Release_Schedule<br />
<br />
<br />
<br />
<br />
C. elegans Synchronisation with GenBank / EMBL:<br />
------------------------------------<br />
<br />
No synchronisation issues<br />
<br />
<br />
C. elegans Chromosomal Changes:<br />
--------------------<br />
There are no changes to the chromosome sequences in this release.<br />
<br />
<br />
C. elegans Gene data set (Live C. elegans genes 47455)<br />
------------------------------------------<br />
Molecular_info 45796 (96.5%)<br />
Concise_description 5849 (12.3%)<br />
Reference 14229 (30%)<br />
WormBase_approved_Gene_name 26336 (55.5%)<br />
RNAi_result 24670 (52%)<br />
Microarray_results 23978 (50.5%)<br />
SAGE_transcript 19180 (40.4%)<br />
<br />
<br />
C. elegans <br />
<br />
Wormpep data set:<br />
----------------------------<br />
<br />
There are 25391 CDSs, from 20484 protein-coding genes<br />
<br />
The 25391 sequences contain base pairs in total.<br />
<br />
Modified entries 266<br />
Deleted entries 105<br />
New entries 252<br />
Reappeared entries 5<br />
<br />
Net change +152<br />
<br />
<br />
C. elegans Genome sequence composition:<br />
----------------------------<br />
<br />
WS228 WS227 change<br />
----------------------------------------------<br />
a 32367418 32367418 +0<br />
c 17780787 17780787 +0<br />
g 17756985 17756985 +0<br />
t 32367086 32367086 +0<br />
n 0 0 +0<br />
- 0 0 +0<br />
<br />
Total 100272276 100272276 +0<br />
<br />
<br />
Pristionchus pacificus Genome sequence composition:<br />
----------------------------<br />
172773083 total<br />
a 43813958<br />
c 32811034<br />
g 32828589<br />
t 43810996<br />
- 0<br />
n 19508506<br />
<br />
<br />
Caenorhabditis remanei Genome sequence composition:<br />
----------------------------<br />
145500347 total<br />
a 42927857<br />
c 26293828<br />
g 26276020<br />
t 42923178<br />
- 0<br />
n 7079464<br />
<br />
<br />
Caenorhabditis japonica Genome sequence composition:<br />
----------------------------<br />
166565019 total<br />
a 46865690<br />
c 30244493<br />
g 30234317<br />
t 46807519<br />
- 0<br />
n 12413000<br />
<br />
<br />
Caenorhabditis briggsae Genome sequence composition:<br />
----------------------------<br />
108419768 total<br />
a 32984239<br />
c 19684682<br />
g 19693545<br />
t 33054090<br />
- 0<br />
n 3003212<br />
<br />
<br />
Caenorhabditis brenneri Genome sequence composition:<br />
----------------------------<br />
190421492 total<br />
a 52222485<br />
c 32837458<br />
g 32882838<br />
t 52164077<br />
- 0<br />
n 20314634<br />
<br />
<br />
<br />
<br />
Tier II Gene counts<br />
---------------------------------------------<br />
pristionchus Gene count 24216 (Coding 24216)<br />
remanei Gene count 32431 (Coding 31471)<br />
japonica Gene count 29962 (Coding 29962)<br />
briggsae Gene count 23050 (Coding 21962)<br />
brenneri Gene count 32257 (Coding 30667)<br />
---------------------------------------------<br />
<br />
<br />
<br />
<br />
-------------------------------------------------<br />
Pristionchus pacificus Protein Stats:<br />
-------------------------------------------------<br />
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)<br />
-------------------------------------------------<br />
Confirmed 229 (0.9%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 4982 (20.6%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 19006 (78.5%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Pristionchus pacificus entries with WormBase-approved Gene name 3169<br />
<br />
<br />
<br />
<br />
-------------------------------------------------<br />
Caenorhabditis remanei Protein Stats:<br />
-------------------------------------------------<br />
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)<br />
-------------------------------------------------<br />
Confirmed 956 (3.0%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 5662 (18.0%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 24858 (79.0%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Caenorhabditis remanei entries with WormBase-approved Gene name 5681<br />
<br />
<br />
<br />
<br />
-------------------------------------------------<br />
Caenorhabditis japonica Protein Stats:<br />
-------------------------------------------------<br />
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)<br />
-------------------------------------------------<br />
Confirmed 176 (0.5%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 578 (1.6%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 35351 (97.9%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Caenorhabditis japonica entries with WormBase-approved Gene name 4682<br />
<br />
<br />
<br />
<br />
-------------------------------------------------<br />
Caenorhabditis briggsae Protein Stats:<br />
-------------------------------------------------<br />
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)<br />
-------------------------------------------------<br />
Confirmed 53 (0.2%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 853 (3.9%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 21080 (95.9%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Status of entries: Protein Accessions<br />
-------------------------------------<br />
UniProtKB accessions 21682 (98.6%)<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Caenorhabditis briggsae entries with WormBase-approved Gene name 5739<br />
<br />
<br />
<br />
<br />
-------------------------------------------------<br />
Caenorhabditis brenneri Protein Stats:<br />
-------------------------------------------------<br />
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)<br />
-------------------------------------------------<br />
Confirmed 1510 (4.9%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 5638 (18.4%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 23522 (76.7%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Caenorhabditis brenneri entries with WormBase-approved Gene name 3260<br />
<br />
<br />
<br />
<br />
-------------------------------------------------<br />
Caenorhabditis elegans Protein Stats:<br />
-------------------------------------------------<br />
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)<br />
-------------------------------------------------<br />
Confirmed 12126 (47.8%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 11232 (44.2%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 2033 (8.0%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Status of entries: Protein Accessions<br />
-------------------------------------<br />
UniProtKB accessions 24610 (96.9%)<br />
<br />
Status of entries: Protein_ID's in EMBL<br />
---------------------------------------<br />
Protein_id 25168 (99.1%)<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Caenorhabditis elegans entries with WormBase-approved Gene name 24724<br />
<br />
<br />
C. elegans Operons Stats<br />
---------------------------------------------<br />
Description: These exist as closely spaced gene clusters similar to bacterial operons<br />
---------------------------------------------<br />
| Live Operons 1254 |<br />
| Genes in Operons 3354 |<br />
---------------------------------------------<br />
<br />
<br />
GO Annotation Stats WS228<br />
--------------------------------------<br />
<br />
GO_codes - used for assigning evidence<br />
--------------------------------------<br />
IC Inferred by Curator<br />
IDA Inferred from Direct Assay<br />
IEA Inferred from Electronic Annotation<br />
IEP Inferred from Expression Pattern<br />
IGI Inferred from Genetic Interaction<br />
IMP Inferred from Mutant Phenotype<br />
IPI Inferred from Physical Interaction<br />
ISS Inferred from Sequence (or Structural) Similarity<br />
NAS Non-traceable Author Statement<br />
ND No Biological Data available<br />
RCA Inferred from Reviewed Computational Analysis<br />
TAS Traceable Author Statement<br />
------------------------------------------------<br />
<br />
Total number of Gene::GO connections: 294345<br />
<br />
Genes Stats:<br />
----------------<br />
Genes with GO_term connections 95532 <br />
IEA GO_code present 89490 <br />
non-IEA GO_code present 6038 <br />
<br />
Source of the mapping data <br />
Source: *RNAi (GFF mapping overlaps) 25676 <br />
*citace 2426 <br />
*Inherited (motif & phenotype) 15087 <br />
<br />
GO_terms Stats:<br />
---------------<br />
Total No. GO_terms 30550 <br />
GO_terms connected to Genes 3384 <br />
GO annotations connected with IEA 1766 <br />
GO annotations connected with non-IEA 1608 <br />
Breakdown IC - 3 IDA - 435 ISS - 147 <br />
IEP - 10 IGI - 137 IMP - 777 <br />
IPI - 77 NAS - 2 ND - 1 <br />
RCA - 0 TAS - 18 <br />
<br />
<br />
-===================================================================================-<br />
<br />
Useful Stats:<br />
---------<br />
<br />
Genes with Sequence and WormBase-approved Gene names<br />
WS228 47255 (24724 elegans / 5739 briggsae / 5681 remanei / 4682 japonica / 3260 brenneri / 3169 pristionchus)<br />
<br />
<br />
-===================================================================================-<br />
<br />
<br />
<br />
New Data:<br />
---------<br />
<br />
Variation_data - <br />
<br />
<br />
Genome sequence updates:<br />
-----------------------<br />
<br />
<br />
New Fixes:<br />
----------<br />
<br />
<br />
Known Problems:<br />
---------------<br />
<br />
<br />
Other Changes:<br />
--------------<br />
<br />
Proposed Changes / Forthcoming Data:<br />
-------------------------------------<br />
<br />
<br />
Model Changes:<br />
------------------------------------<br />
<br />
<br />
For more info mail worm@sanger.ac.uk<br />
-===================================================================================-<br />
<br />
<br />
Quick installation guide for UNIX/Linux systems<br />
-----------------------------------------------<br />
<br />
1. Create a new directory to contain your copy of WormBase,<br />
e.g. /users/yourname/wormbase<br />
<br />
2. Unpack and untar all of the database.*.tar.gz files into<br />
this directory. You will need approximately 2-3 Gb of disk space.<br />
<br />
3. Obtain and install a suitable acedb binary for your system<br />
(available from www.acedb.org).<br />
<br />
4. Use the acedb 'xace' program to open your database, e.g.<br />
type 'xace /users/yourname/wormbase' at the command prompt.<br />
<br />
5. See the acedb website for more information about acedb and<br />
using xace.<br />
<br />
____________ END _____________<br />
<br />
</pre><br />
<br />
=== Bug Fixes ===</div>
Pdavis