https://wiki.biouml.org/index.php?action=history&feed=atom&title=Mutation_effect_on_sites_advanced_%28analysis%29 2026-04-13T03:19:53Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=Mutation_effect_on_sites_advanced_(analysis)&diff=8794&oldid=prev 2020-12-09T11:14:52Z

<p>Protected &quot;<a href="/index.php/Mutation_effect_on_sites_advanced_(analysis)" title="Mutation effect on sites advanced (analysis)">Mutation effect on sites advanced (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 11:14, 9 December 2020</td> </tr></table>

WikiBot https://wiki.biouml.org/index.php?title=Mutation_effect_on_sites_advanced_(analysis)&diff=8790&oldid=prev 2020-12-09T11:14:52Z

<p>Automatic synchronization with BioUML</p> <p><b>New page</b></p><div>;Analysis title<br /> :[[File:GTRD-Mutation-effect-on-sites-advanced-icon.png]] Mutation effect on sites advanced<br /> ;Provider<br /> :[[Institute of Systems Biology]]<br /> ;Class<br /> :{{Class|biouml.plugins.gtrd.analysis.maos.MutationAffectOnSitesAdvanced}}<br /> ;Plugin<br /> :[[Biouml.plugins.gtrd (plugin)|biouml.plugins.gtrd (GTRD)]]<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 type''' – The type of position weight matrix score<br /> * '''Score difference''' – Minimal site score difference between reference and alternative sequences<br /> * '''Independent variations''' – Treat each variation independently<br /> * '''Target gene TSS upstream''' – When searching for target genes, match TF binding sites to this distance upstream of TSS.<br /> * '''Target gene TSS downstream''' – When searching for target genes, match TF binding sites to this distance downstream of TSS.<br /> * '''One nearest target gene''' – Report only one target gene nearest to TSS.<br /> * '''TF class depth''' – TF class depth<br /> * '''Add transpath annotation''' – Transpath pathways annotation will be added to the output table<br /> * '''Transpath''' – Transpath<br /> * '''Add HumanPSD annotation''' – HumanPSD disease annotation will be added to the output table<br /> * '''HumanPSD''' – HumanPSD<br /> * '''Output table''' – Output table<br /> * '''Site gain track''' – Resulting track with site gain events<br /> * '''Site loss track''' – Resulting track with site gain events<br /> * '''Important mutations''' – Track of mutations that affects binding sites<br /> * '''Summary table''' – Summary table giving site model frequencies per mutation<br /> * '''Selected GTRD peaks/metaclusters''' – Selected GTRD peaks/metaclusters<br /> <br /> [[Category:Analyses]]<br /> [[Category:GTRD (analyses group)]]<br /> [[Category:ISB analyses]]<br /> [[Category:Autogenerated pages]]</div>

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