https://wiki.biouml.org/index.php?action=history&feed=atom&title=Mutation_effect_on_sites_%28analysis%29 2026-04-13T10:09:46Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=Mutation_effect_on_sites_(analysis)&diff=8947&oldid=prev 2020-12-09T11:15:17Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 11:15, 9 December 2020</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Analysis title</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Analysis title</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:[[File:<del class="diffchange diffchange-inline">BSA</del>-Mutation-effect-on-sites-icon.png]] Mutation effect on sites</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:[[File:<ins class="diffchange diffchange-inline">Mutations</ins>-Mutation-effect-on-sites-icon.png]] Mutation effect on sites</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Institute of Systems Biology]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Institute of Systems Biology]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Class</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Class</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:{{Class|ru.biosoft.bsa.analysis.MutationEffectOnSites}}</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:{{Class|ru.biosoft.bsa.analysis<ins class="diffchange diffchange-inline">.maos</ins>.MutationEffectOnSites}}</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Plugin</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Plugin</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Description ====</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Description ====</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Find transcription factor <del class="diffchange diffchange-inline">binsing </del>sites affected by mutations</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Find transcription factor <ins class="diffchange diffchange-inline">binding </ins>sites affected by mutations<ins class="diffchange diffchange-inline">.</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Parameters: ====</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Parameters: ====</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 18:</td> <td colspan="2" class="diff-lineno">Line 18:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequence collection''' – Specify path to folder containing sequences if &lt;nowiki&gt;'&lt;/nowiki&gt;Custom&lt;nowiki&gt;'&lt;/nowiki&gt; sequences source is selected</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''Sequence collection''' – Specify path to folder containing sequences if &lt;nowiki&gt;'&lt;/nowiki&gt;Custom&lt;nowiki&gt;'&lt;/nowiki&gt; sequences source is selected</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Profile''' – Predefined set of site models</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Profile''' – Predefined set of site models</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* '''Score type''' – The type of position weight matrix score</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Score difference''' – Minimal site score difference between reference and alternative sequences</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Score difference''' – Minimal site score difference between reference and alternative sequences</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* '''Independent variations''' – Treat each variation independently</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* '''Target gene TSS upstream''' – When searching for target genes, match TF binding sites to this distance upstream of TSS.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* '''Target gene TSS downstream''' – When searching for target genes, match TF binding sites to this distance downstream of TSS.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* '''One nearest target gene''' – Report only one target gene nearest to TSS.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* '''Output table''' – Output table</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Site gain track''' – Resulting track with site gain events</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Site gain track''' – Resulting track with site gain events</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Site loss track''' – Resulting track with site gain events</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Site loss track''' – Resulting track with site gain events</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* '''Important mutations''' – Track of mutations that affects binding sites</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Summary table''' – Summary table giving site model frequencies per mutation</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Summary table''' – Summary table giving site model frequencies per mutation</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Analyses]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Analyses]]</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Category:<del class="diffchange diffchange-inline">BSA </del>(analyses group)]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Category:<ins class="diffchange diffchange-inline">Mutations </ins>(analyses group)]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:ISB analyses]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:ISB analyses]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Autogenerated pages]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Autogenerated pages]]</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Mutation_effect_on_sites_(analysis)&diff=6931&oldid=prev 2017-02-13T11:59:58Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 11:59, 13 February 2017</td> </tr><tr><td colspan="2" class="diff-lineno">Line 19:</td> <td colspan="2" class="diff-lineno">Line 19:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Profile''' – Predefined set of site models</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Profile''' – Predefined set of site models</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Score difference''' – Minimal site score difference between reference and alternative sequences</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Score difference''' – Minimal site score difference between reference and alternative sequences</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* '''<del class="diffchange diffchange-inline">Output </del>track''' – <del class="diffchange diffchange-inline">Track </del>with <del class="diffchange diffchange-inline">affected sites</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''<ins class="diffchange diffchange-inline">Site gain </ins>track''' – <ins class="diffchange diffchange-inline">Resulting track </ins>with <ins class="diffchange diffchange-inline">site gain events</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* '''Site loss track''' – Resulting track with site gain events</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* '''Summary table''' – Summary table giving site model frequencies per mutation</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Analyses]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Analyses]]</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Mutation_effect_on_sites_(analysis)&diff=5756&oldid=prev 2014-12-11T09:17:05Z

<p>Protected &quot;<a href="/index.php/Mutation_effect_on_sites_(analysis)" title="Mutation effect on sites (analysis)">Mutation effect on sites (analysis)</a>&quot;: Autogenerated page (‎[edit=sysop] (indefinite))</p> <table class='diff diff-contentalign-left'> <tr style='vertical-align: top;'> <td colspan='1' style="background-color: white; color:black;">← Older revision</td> <td colspan='1' style="background-color: white; color:black;">Revision as of 09:17, 11 December 2014</td> </tr></table>

WikiBot https://wiki.biouml.org/index.php?title=Mutation_effect_on_sites_(analysis)&diff=5752&oldid=prev 2014-12-11T09:16:59Z

<p>Automatic synchronization with BioUML</p> <p><b>New page</b></p><div>;Analysis title<br /> :[[File:BSA-Mutation-effect-on-sites-icon.png]] Mutation effect on sites<br /> ;Provider<br /> :[[Institute of Systems Biology]]<br /> ;Class<br /> :{{Class|ru.biosoft.bsa.analysis.MutationEffectOnSites}}<br /> ;Plugin<br /> :[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]<br /> <br /> ==== Description ====<br /> Find transcription factor binsing sites affected by mutations<br /> <br /> ==== Parameters: ====<br /> <br /> * '''Input VCF track''' – Input track in VCF format<br /> * '''Genome''' – Reference genome<br /> ** '''Sequences source''' – Select database to get sequences from or &lt;nowiki&gt;'&lt;/nowiki&gt;Custom&lt;nowiki&gt;'&lt;/nowiki&gt; to specify sequences location manually<br /> ** '''Sequence collection''' – Specify path to folder containing sequences if &lt;nowiki&gt;'&lt;/nowiki&gt;Custom&lt;nowiki&gt;'&lt;/nowiki&gt; sequences source is selected<br /> * '''Profile''' – Predefined set of site models<br /> * '''Score difference''' – Minimal site score difference between reference and alternative sequences<br /> * '''Output track''' – Track with affected sites<br /> <br /> [[Category:Analyses]]<br /> [[Category:BSA (analyses group)]]<br /> [[Category:ISB analyses]]<br /> [[Category:Autogenerated pages]]</div>

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