Difference between revisions of "Prediction of TF-binding sites of given TF (analysis)"
From BioUML platform
m (Protected "Prediction of TF-binding sites of given TF (analysis)": Autogenerated page ([edit=sysop] (indefinite))) |
(Automatic synchronization with BioUML) |
||
| Line 18: | Line 18: | ||
* '''Genome fragment type''' – Select type of genome fragments in which sites will be predicted | * '''Genome fragment type''' – Select type of genome fragments in which sites will be predicted | ||
* '''Site name''' – Name of predicted sites | * '''Site name''' – Name of predicted sites | ||
| − | * '''Type of site model''' – | + | * '''Type of site model''' – Select type of site model |
* '''Matrices and thresholds''' – Define matrices and thresholds | * '''Matrices and thresholds''' – Define matrices and thresholds | ||
* '''Chromosome''' – Chromosome | * '''Chromosome''' – Chromosome | ||
* '''Start position''' – Start position of chromosome fragment | * '''Start position''' – Start position of chromosome fragment | ||
* '''Finish position''' – Finish position of chromosome fragment | * '''Finish position''' – Finish position of chromosome fragment | ||
| − | * '''Input track''' – Select input ChIP-seq track | + | * '''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 | * '''Minimal region length''' – Minimal length of sequence region | ||
* '''Path to output track''' – Path to output track | * '''Path to output track''' – Path to output track | ||
Latest revision as of 19:00, 13 February 2017
- 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)
[edit] Description
Prediction of TF-binding sites of given TF in given chromosome fragment by siteModel of given type
[edit] 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
