https://wiki.wormbase.org/index.php?title=WS219&feed=atom&action=history
WS219 - Revision history
2024-03-29T15:38:05Z
Revision history for this page on the wiki
MediaWiki 1.33.0
https://wiki.wormbase.org/index.php?title=WS219&diff=13198&oldid=prev
Pdavis at 11:11, 21 December 2011
2011-12-21T11:11:09Z
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 11:11, 21 December 2011</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l4" >Line 4:</td>
<td colspan="2" class="diff-lineno">Line 4:</td></tr>
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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>WS219 was built by [Michael Paulini (michael.paulini@<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>WS219 was built by [Michael Paulini (michael.paulini@<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>
<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>The WS219 build directory includes:</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>The WS219 build directory includes:</div></td></tr>
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<td colspan="2" class="diff-lineno">Line 427:</td></tr>
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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>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">help</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>
<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>
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Pdavis
https://wiki.wormbase.org/index.php?title=WS219&diff=6820&oldid=prev
Mh6 at 09:18, 6 October 2010
2010-10-06T09:18:40Z
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 09:18, 6 October 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l22" >Line 22:</td>
<td colspan="2" class="diff-lineno">Line 22:</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> i) confirmed_genes.WS219.gz - DNA sequences of all genes confirmed by EST &/or cDNA</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> i) confirmed_genes.WS219.gz - DNA sequences of all genes confirmed by EST &/or cDNA</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> ii) cDNA2orf.WS219.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)</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> ii) cDNA2orf.WS219.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)</div></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> iii) geneIDs.WS219.gz - list of all <del class="diffchange diffchange-inline">current </del>gene identifiers with CGC & molecular names (when known)</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> iii) geneIDs.WS219.gz - list of all <ins class="diffchange diffchange-inline">currentnt </ins>gene identifiers with CGC & molecular names (when known)</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> iv) PCR_product2gene.WS219.gz - Mappings between PCR products and overlapping Genes</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> iv) PCR_product2gene.WS219.gz - Mappings between PCR products and overlapping Genes</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> v) oligo_mapping.gz - V </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> v) oligo_mapping.gz - V </div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l268" >Line 268:</td>
<td colspan="2" class="diff-lineno">Line 268:</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>
<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>Caenorhabditis brenneri entries with WormBase-approved Gene name 3091</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>Caenorhabditis brenneri entries with WormBase-approved Gene name 3091</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;"></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;"></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;">Caenorhabditis elegans Protein Stats:</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;">Status of entries: Confidence level of prediction (based on the amount of transcript evidence)</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;">Confirmed 11654 (46.9%) Every base of every exon has transcription evidence (mRNA, EST etc.)</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;">Partially_confirmed 10997 (44.3%) Some, but not all exon bases are covered by transcript evidence</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;">Predicted 2175 (8.8%) No transcriptional evidence at all</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;"></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;">Status of entries: Protein Accessions</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;">UniProtKB accessions 24631 (99.2%)</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;">Status of entries: Protein_ID's in EMBL</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;">Protein_id 24631 (99.2%)</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;">Gene <-> CDS,Transcript,Pseudogene connections</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;">Caenorhabditis elegans entries with WormBase-approved Gene name 24430</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 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;"></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>
</table>
Mh6
https://wiki.wormbase.org/index.php?title=WS219&diff=6817&oldid=prev
Mh6: Created page with '= Release Letter = <pre> New release of WormBase WS219, Wormpep219 and Wormrna219 Tue Oct 5 16:04:14 BST 2010 WS219 was built by [Michael Paulini (michael.paulini@sanger.ac.uk…'
2010-10-05T16:02:50Z
<p>Created page with '= Release Letter = <pre> New release of WormBase WS219, Wormpep219 and Wormrna219 Tue Oct 5 16:04:14 BST 2010 WS219 was built by [Michael Paulini (michael.paulini@sanger.ac.uk…'</p>
<p><b>New page</b></p><div>= Release Letter =<br />
<pre><br />
New release of WormBase WS219, Wormpep219 and Wormrna219 Tue Oct 5 16:04:14 BST 2010<br />
<br />
<br />
WS219 was built by [Michael Paulini (michael.paulini@sanger.ac.uk)]<br />
-===================================================================================-<br />
The WS219 build directory includes:<br />
genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data<br />
genomes/b_malayi: - genome_feature_tables/ sequences/<br />
genomes/c_brenneri: - genome_feature_tables/ sequences/<br />
genomes/c_briggsae: - genome_feature_tables/ sequences/<br />
genomes/c_elegans: - annotation/ genome_feature_tables/ sequences/<br />
genomes/c_japonica: - genome_feature_tables/ sequences/<br />
genomes/c_remanei: - genome_feature_tables/ sequences/<br />
genomes/h_bacteriophora: - genome_feature_tables/ sequences/<br />
genomes/h_contortus: - genome_feature_tables/ sequences/<br />
genomes/m_hapla: - genome_feature_tables/ sequences/<br />
genomes/m_incognita: - sequences/<br />
genomes/p_pacificus: - genome_feature_tables/ sequences/<br />
*annotation/ - contains additional annotations<br />
i) confirmed_genes.WS219.gz - DNA sequences of all genes confirmed by EST &/or cDNA<br />
ii) cDNA2orf.WS219.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)<br />
iii) geneIDs.WS219.gz - list of all current gene identifiers with CGC & molecular names (when known)<br />
iv) PCR_product2gene.WS219.gz - Mappings between PCR products and overlapping Genes<br />
v) oligo_mapping.gz - V <br />
*genome_feature_tables/ - contains the main .gff files and supplementary .gff data<br />
*sequences/ - contains dna/ protein/ rna/ sub dirs<br />
sequences/protein - WormBase protein set for species + history etc.<br />
vi) wormpep219.tar.gz - full Wormpep distribution corresponding to WS219<br />
vii) wormrna219.tar.gz - latest WormRNA release containing non-coding RNA's in the genome<br />
viii) best_blastp_hits_species.WS219.gz - for each C. elegans WormPep protein, lists Best blastp match to<br />
human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins.<br />
sequences/dna - WormBase dna data genomic sequence (raw, soft_masked masked), agp<br />
ix) intergenic_sequences.dna.gz<br />
sequences/rna - WormBase rna gene data.<br />
acedb DIR - Everything needed to generate a local copy of the The Primary database<br />
x) database.WS219.*.tar.gz - compressed acedb database for new release<br />
xi) models.wrm.WS219 - the latest database schema (also in above database files)<br />
xii) WS219-WS218.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 - compara.tar.bz2 wormpep217_clw.sql.bz2<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 40117)<br />
------------------------------------------<br />
Molecular_info 38438 (95.8%)<br />
Concise_description 5692 (14.2%)<br />
Reference 14098 (35.1%)<br />
WormBase_approved_Gene_name 26062 (65%)<br />
RNAi_result 22875 (57%)<br />
Microarray_results 21042 (52.5%)<br />
SAGE_transcript 19152 (47.7%)<br />
<br />
<br />
C. elegans <br />
<br />
Wormpep data set:<br />
----------------------------<br />
<br />
There are 20408 CDS in autoace, 24826 when counting 4418 alternate splice forms.<br />
<br />
The 24826 sequences contain 10,921,490 base pairs in total.<br />
<br />
Modified entries 25<br />
Deleted entries 36<br />
New entries 101<br />
Reappeared entries 1<br />
<br />
Net change +66<br />
The differnce between the total CDS's of this (24826) and the last build (24761) does not equal the net change 66<br />
Please investigate! ! <br />
<br />
<br />
C. elegans Genome sequence composition:<br />
----------------------------<br />
<br />
WS219 WS218 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 />
169822619 total<br />
a 41799168<br />
c 31168435<br />
g 31196239<br />
t 41802890<br />
- 0<br />
n 23855887<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 />
163282347 total<br />
a 39053092<br />
c 25603225<br />
g 25576971<br />
t 39126103<br />
- 0<br />
n 33922956<br />
<br />
<br />
Caenorhabditis briggsae Genome sequence composition:<br />
----------------------------<br />
108478630 total<br />
a 33004189<br />
c 19675861<br />
g 19707411<br />
t 33049803<br />
- 59500<br />
n 2981866<br />
<br />
<br />
Caenorhabditis brenneri Genome sequence composition:<br />
----------------------------<br />
190426650 total<br />
a 52223359<br />
c 32838518<br />
g 32883836<br />
t 52164943<br />
- 0<br />
n 20315994<br />
<br />
<br />
<br />
<br />
Tier II Gene counts<br />
---------------------------------------------<br />
pristionchus Gene count 29638 (Coding 29639)<br />
remanei Gene count 32431 (Coding 31476)<br />
heterorhabditis Gene count 0 (Coding 0)<br />
japonica Gene count 27177 (Coding 25870)<br />
briggsae Gene count 23043 (Coding 21995)<br />
brenneri Gene count 32295 (Coding 30707)<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 425 (1.4%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 5309 (17.9%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 23905 (80.7%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Pristionchus pacificus entries with WormBase-approved Gene name 2792<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 955 (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 24859 (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 5461<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 1182 (4.6%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 4974 (19.2%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 19714 (76.2%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Caenorhabditis japonica entries with WormBase-approved Gene name 4791<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 52 (0.2%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 856 (3.9%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 21087 (95.9%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Status of entries: Protein Accessions<br />
-------------------------------------<br />
UniProtKB accessions 21708 (98.7%)<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Caenorhabditis briggsae entries with WormBase-approved Gene name 5497<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 1517 (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 23550 (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 3091<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 1288 |<br />
| Genes in Operons 3343 |<br />
<br />
<br />
<br />
GO Annotation Stats WS219<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 />
NDNo Biological Data available<br />
RCA ?<br />
TAS Traceable Author Statement<br />
------------------------------------------------<br />
<br />
Total number of Gene::GO connections: 262467<br />
<br />
Genes Stats:<br />
----------------<br />
Genes with GO_term connections 88452 <br />
IEA GO_code present 83023 <br />
non-IEA GO_code present 5425 <br />
<br />
Source of the mapping data <br />
Source: *RNAi (GFF mapping overlaps) 23372 <br />
*citace 2133 <br />
*Inherited (motif & phenotype) 14290 <br />
<br />
GO_terms Stats:<br />
---------------<br />
Total No. GO_terms 30467 <br />
GO_terms connected to Genes 3241 <br />
GO annotations connected with IEA 1838 <br />
GO annotations connected with non-IEA 1399 <br />
Breakdown IC - 2 IDA - 348 ISS - 126 <br />
IEP - 9 IGI - 112 IMP - 711 <br />
IPI - 68 NAS - 1 ND - 1 <br />
RCA - 0 TAS - 21 <br />
<br />
<br />
-===================================================================================-<br />
<br />
Useful Stats:<br />
---------<br />
<br />
Genes with Sequence and CGC name<br />
WS219 46062 (24430 elegans / 5497 briggsae / 5461 remanei / 4791 japonica / 3091 brenneri / 2792 pristionchus)<br />
<br />
<br />
-===================================================================================-<br />
<br />
<br />
<br />
New Data:<br />
---------<br />
There is a new file produced on the Sanger FTP site.<br />
<br />
requested by : Megan Senchuk, msenchuk@mcb.harvard.edu<br />
<br />
function: a 'nice' view of the phenotypes produced by genes knocked down by RNAi.<br />
<br />
script : ONTOLOGY/get_easy_phenotypes.pl<br />
<br />
output1 : ftp://ftp.sanger.ac.uk/pub/wormbase/WSXXX/ONTOLOGY/rnai_phenotypes.WSXXX.wb<br />
<br />
example lines :<br />
<br />
WBGene00001908 F17E9.9 larval arrest WBPhenotype:0000059 WBRNAi00025129|WBPaper00006395<br />
<br />
WBGene00001908 F17E9.9 locomotion variant WBPhenotype:0000643 WBRNAi00025129|WBPaper00006395<br />
<br />
output2 : ftp://ftp.sanger.ac.uk/pub/wormbase/WSXXX/ONTOLOGY/rnai_phenotypes_quick.WXXX.wb<br />
<br />
example lines :<br />
<br />
WBGene00001908 F17E9.9 larval arrest, locomotion variant, embryonic lethal, maternal sterile<br />
<br />
WBGene00019433 K06A5.6 embryonic lethal<br />
<br />
<br />
Genome sequence updates:<br />
-----------------------<br />
The C.brenneri assembly had contaminations removed and was updated to the latest version<br />
available in GenBank/EMBLBank/DDBJ.<br />
<br />
New Fixes:<br />
----------<br />
C.brenneri genes on the removed sequences were killed.<br />
<br />
Known Problems:<br />
---------------<br />
<br />
<br />
Other Changes:<br />
--------------<br />
<br />
Proposed Changes / Forthcoming Data:<br />
-------------------------------------<br />
?Strain class<br />
Removed:Extended_genotype ?Variation<br />
<br />
Comment: Removed this unused tag structure as data can be stored in current<br />
tags and the additional information/context can be resolved at the<br />
display level.<br />
<br />
Model Changes:<br />
------------------------------------<br />
?Molecule - fix ?Phenotype tags missed from original submission + additions (Karen Y.)<br />
<br />
?Strain - Extended_genotype - signed off on the call, but had errors I discovered on testing.<br />
Dropped the XREF back to Variation<br />
<br />
?Variation removal of obsolete/unused tags (Mary Ann T., Jolene F.)<br />
<br />
?Phenotype - Migration of data from "Not" tags continues need additional tags for storing phenotypes scored but not observed (Wen C.)<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></div>
Mh6