Prediction of TF-binding sites of given TF (analysis)
From BioUML platform
- Analysis title
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
