Remove overlapping sites (analysis) - Revision history

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2020-12-09T11:15:20Z

Automatic synchronization with BioUML

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Automatic synchronization with BioUML

WikiBot: Protected "Remove overlapping sites (analysis)": Autogenerated page (‎[edit=sysop] (indefinite))

2014-12-11T09:17:07Z

Protected "Remove overlapping sites (analysis)": Autogenerated page (‎[edit=sysop] (indefinite))

WikiBot: Automatic synchronization with BioUML

2014-12-11T09:17:05Z

Automatic synchronization with BioUML

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;Analysis title
:[[File:Default-analysis-icon.png]] Remove overlapping sites
;Provider
:[[Institute of Systems Biology]]
;Class
:{{Class|ru.biosoft.bsa.analysis.FilterOverlappingSites}}
;Plugin
:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]

==== Description ====
Constructs subset of input track so that no sites overlap in the output track. The <nowiki>'</nowiki>Overlapping site selection mode<nowiki>'</nowiki> parameter controls wich sites will be selected from the set of overlapping sites. <nowiki>'</nowiki>One longest<nowiki>'</nowiki>, <nowiki>'</nowiki>One shortest<nowiki>'</nowiki>, <nowiki>'</nowiki>One with best value<nowiki>'</nowiki> and <nowiki>'</nowiki>One random<nowiki>'</nowiki> modes will select single site from the set of overlapping sites. Other modes can select more then one site from the set of overlapping sites, but resulting sites will not overlap each other. <nowiki>'</nowiki>Largest set<nowiki>'</nowiki> mode constructs non-overlapping set of sites with maximal number of sites. <nowiki>'</nowiki>Longest set<nowiki>'</nowiki> mode constructs non-overlapping set with largest total length of sites. <nowiki>'</nowiki>Set of best sites<nowiki>'</nowiki> mode iteratively selects the best site and removes sites that overlap best site, then selects the best from remaining and removes sites that overlap best site, and so on until no sites remain.

==== Parameters: ====

* '''Input track''' – Track to filter
* '''Genome''' – Reference genome
** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected
* '''Independent strands''' – Handle sites from different strands independently
* '''Overlapping site selection mode''' – How to select sites from the set overlapping sites
* '''Leading property''' – Site property to be used for site selection
* '''Best value type''' – What is the best value of leading property?
* '''Output track''' – Resulting track

[[Category:Analyses]]
[[Category:BSA (analyses group)]]
[[Category:ISB analyses]]
[[Category:Autogenerated pages]]

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 ;Analysis title
-:[[File:BSA-Remove-overlapping-sites-icon.png]] Remove overlapping sites
+:[[File:Operations-with-genomic-tracks-Remove-overlapping-sites-icon.png]] Remove overlapping sites
 ;Provider
 :[[Institute of Systems Biology]]
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 [[Category:Analyses]]
-[[Category:BSA (analyses group)]]
+[[Category:Operations with genomic tracks (analyses group)]]
 [[Category:ISB analyses]]
 [[Category:Autogenerated pages]]