Construct composite modules (analysis)

From BioUML platform
Revision as of 16:16, 11 December 2014 by BioUML wiki Bot (Talk | contribs)

Jump to: navigation, search
Analysis title
BSA-Construct-composite-modules-icon.png Construct composite modules
Provider
geneXplain GmbH
Class
CMAAnalysis
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
      • Pairs mode – Whether the sites of at least two different site models satisfying the cut-off condition must be present on the sequence
  • Output path – Path to store result
Personal tools
Namespaces

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