Matrix derivation (analysis)

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