View source for Prediction of TF-binding sites of given TF (analysis)

;Analysis title
:[[File:Default-analysis-icon.png]] Prediction of TF-binding sites of given TF
;Provider
:[[Institute of Systems Biology]]
;Class
:{{Class|biouml.plugins.bindingregions.analysis.SiteModelPredictionInGenome}}
;Plugin
:[[Biouml.plugins.bindingregions (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 <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> 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

[[Category:Analyses]]
[[Category:Binding regions (analyses group)]]
[[Category:ISB analyses]]
[[Category:Autogenerated pages]]