Difference between revisions of "Remove overlapping sites (analysis)"

From BioUML platform
Jump to: navigation, search
(Automatic synchronization with BioUML)
 
(Automatic synchronization with BioUML)
 
(2 intermediate revisions by one user not shown)
Line 1: Line 1:
 
;Analysis title
 
;Analysis title
:[[File:Default-analysis-icon.png]] Remove overlapping sites
+
:[[File:Operations-with-genomic-tracks-Remove-overlapping-sites-icon.png]] Remove overlapping sites
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
Line 24: Line 24:
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]
[[Category:BSA (analyses group)]]
+
[[Category:Operations with genomic tracks (analyses group)]]
 
[[Category:ISB analyses]]
 
[[Category:ISB analyses]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

Latest revision as of 18:15, 9 December 2020

Analysis title
Operations-with-genomic-tracks-Remove-overlapping-sites-icon.png Remove overlapping sites
Provider
Institute of Systems Biology
Class
FilterOverlappingSites
Plugin
ru.biosoft.bsa (Bio-sequences analyses plugin)

[edit] Description

Constructs subset of input track so that no sites overlap in the output track. The 'Overlapping site selection mode' parameter controls wich sites will be selected from the set of overlapping sites. 'One longest', 'One shortest', 'One with best value' and 'One random' 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. 'Largest set' mode constructs non-overlapping set of sites with maximal number of sites. 'Longest set' mode constructs non-overlapping set with largest total length of sites. 'Set of best sites' 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.

[edit] Parameters:

  • Input track – Track to filter
  • Genome – Reference genome
    • Sequences source – Select database to get sequences from or 'Custom' to specify sequences location manually
    • Sequence collection – Specify path to folder containing sequences if 'Custom' 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
Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox