TF binding sites prediction in genome or track (analysis)

Analysis title

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