TF binding sites prediction in genome or track (analysis)

From BioUML platform
Jump to: navigation, search
Analysis title
Default-analysis-icon.png TF binding sites prediction in genome or track
Provider
Institute of Systems Biology
Class
SitePredictionInGenome
Plugin
biouml.plugins.bindingregions (Binding-regions related analyses)

Description

Prediction of TF-binding sites of given TF in whole genome or in given chromosome fragment or in ChIP-Seq dataset. Sites are predicted by different PWM-methods

Parameters:

  • Sequence set type – Select type of sequences
  • 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
  • Chromosome name – Select chromosome name
  • Start position – Start position of chromosome fragment
  • Finish position – Finish position of chromosome fragment
  • Path to track – Path to track with ChIP-Seq dataset
  • Site name – Name of predicted sites
  • Prediction models – Define prediction models
  • The output track name – The output track name
  • Path to output folder – Path to output folder
Personal tools
Namespaces

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