Matrix derivation (analysis)
From BioUML platform
- Analysis title
- Matrix derivation
- Provider
- Institute of Systems Biology
- Class
MatrixDerivation
- Plugin
- biouml.plugins.bindingregions (Binding-regions related analyses)
Description
Calculation of matrices by using mixture of normal components for scores of best sites in given sequence sample
Parameters:
- Name of algorithm – Select name of algorithm
- Type of site model – Select type of site model that will be used for matrix derivation
- Window size – Window size
- Are both strands? – Do analize both strands of sequences? (if 'no', then only strand (+) will be analyzed)
- Path to table with sequence sample – Select path to table with sequence sample
- Name of table column with sequence sample – Select name of table column with sequence sample
- Parameters specific for 'Matrix derivation : successive algorithm based on 2-component normal mixtures' – Parameters specific for 'Matrix derivation : successive algorithm based on 2-component normal mixtures'
- P-value threshold – P-value threshold
- Number of matrices – How many matrices will be constructed
- Initial approximation for matix – Define initial approximation for matix
- Initial matrix approximation type – Select type of initial matrix approximation
- Consensus – Specify the consensus
- Matrix name – Define matrix name
- Matrix path – Specify the path to the initial matrix
- Parameters specific for 'Matrix derivation : EM-like algorithm for identification of several matrices simultaneously' – Parameters specific for 'Matrix derivation : EM-like algorithm for identification of several matrices simultaneously'
- Score threshold – Score threshold
- Initial approximations for matices – Define initial approximations for matices
- Maximal number of iterations – Maximal number of iterations in algorithm
- Path to output folder – Output folder will be created under this location when it doesn't exist