Difference between revisions of "Construct composite modules (analysis)"

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;Analysis title
 
;Analysis title
:[[File:BSA-Construct-composite-modules-icon.png]] Construct composite modules
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:[[File:Construct-composite-modules-analysis-icon.png]] Construct composite modules
 
;Provider
 
;Provider
 
:[[geneXplain GmbH]]
 
:[[geneXplain GmbH]]

Revision as of 12:32, 16 May 2013

Analysis title
File:Construct-composite-modules-analysis-icon.png Construct composite modules
Provider
geneXplain GmbH
Plugin
biouml.plugins.cma (Composite module analyst)

Description

Predict composite module using the result of the "Site search on gene set" analysis.

Parameters:

  • Site search result – Result of previous site search run with background track
  • Genetic algorithm parameters (expert) – Genetic algorithm parameters
    • Number of iterations – Number of iterations
    • Population size – Population size
    • Non-change limit – Number of iterations to stop after if best score is not improved
    • Elite size – Number of elite organisms (i.e. best organisms to survive unconditionally)
    • Mutation rate – This controls how often mutation occurs and how significant they are (0..1)
  • Score calculation parameters (expert) – Parameters which control score calculation
    • Penalty rate – Which penalty value will be assigned
    • Site models in focus – At least one of these models must present in the resulting composite model to have non-zero score
    • All modules contain site model in focus – If checked, then each module must contain at least one site model from the focus
    • Focused sequences percent – Minimal percent of sequences in yes-set which actually contains sites of site models in focus
  • Model parameters – Model parameters
    • Min modules – Minimal number of modules
    • Max modules – Maximal number of modules
    • Gaussian model (expert) – Gaussian model
      • Min models – Minimal number of site models in module
      • Max models – Maximal number of site models in module
      • Min sites to account – Minimal number of sites to account
      • Max sites to account – Maximal number of sites to account
      • Min module width – Minimal width (sigma) of the module
      • Max module width – Maximal width (sigma) of the module
  • Output path – Path to store result
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