Prediction of TF-binding sites of given TF (analysis)

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Analysis title
Default-analysis-icon.png Prediction of TF-binding sites of given TF
Provider
Institute of Systems Biology
Class
SiteModelPredictionInGenome
Plugin
biouml.plugins.bindingregions (Binding-regions related analyses)

Description

Prediction of TF-binding sites of given TF in given chromosome fragment by siteModel of given type

Parameters:

  • Sequences collection – Select a source of nucleotide sequences
    • 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
  • Genome fragment type – Select type of genome fragments in which sites will be predicted
  • Site name – Name of predicted sites
  • Type of site model – Select type of site model
  • Matrices and thresholds – Define matrices and thresholds
  • Chromosome – Chromosome
  • Start position – Start position of chromosome fragment
  • Finish position – Finish position of chromosome fragment
  • Input track – Select input track (it can be ChIP-seq track from GTRD; thus, it can be the result of MACS or SISSRs peak-finder)
  • Minimal region length – Minimal length of sequence region
  • Path to output track – Path to output track
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