Construct composite modules on tracks (analysis)

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Analysis title
Composite-module-analyses-Construct-composite-modules-on-tracks-icon.png Construct composite modules on tracks
geneXplain GmbH
biouml.plugins.cma (Composite module analyst)


Predicts composite module using the result of the "Site search on track" analysis. Composite modules - combinations of binding sites common for promoters of functionally related genes and responsible for the major component of the gene expression pattern of these genes. For more information see [1].


  • Experiment track – Path to experiment ('yes') track
  • Control track – Path to control ('no') 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
    • Site models in focus table (expert) – The table of site models in focus
    • 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
    • Sequence column – Column to take sequences from
    • Sequences in focus – Selected sequences should be in the result top
    • Top sequences size (percent) – Size of sequences (in percent) that will be considered as top
    • Sequences in focus in top (percent) – Minimal percent of sequences in focus in the top
  • 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


  1. Alexander Kel, Tatiana Konovalova, Tagir Valeev, Evgeny Cheremushkin, Olga Kel-Margoulis, Edgar Wingender. Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations. Bioinformatics. 2006 May 15; 22(10):1190-7. Epub 2006 Feb 10. doi: 10.1093/bioinformatics/btl041
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