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Protected "Matrix derivation (analysis)": Autogenerated page (‎[edit=sysop] (indefinite))

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2017-02-13T12:00:13Z

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;Analysis title
:[[File:Default-analysis-icon.png]] Matrix derivation
;Provider
:[[Institute of Systems Biology]]
;Class
:{{Class|biouml.plugins.bindingregions.analysis.MatrixDerivation}}
;Plugin
:[[Biouml.plugins.bindingregions (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 <nowiki>'</nowiki>no<nowiki>'</nowiki>, 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 <nowiki>'</nowiki>Matrix derivation : successive algorithm based on 2-component normal mixtures<nowiki>'</nowiki>''' – Parameters specific for <nowiki>'</nowiki>Matrix derivation : successive algorithm based on 2-component normal mixtures<nowiki>'</nowiki>
** '''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 <nowiki>'</nowiki>Matrix derivation : EM-like algorithm for identification of several matrices simultaneously<nowiki>'</nowiki>''' – Parameters specific for <nowiki>'</nowiki>Matrix derivation : EM-like algorithm for identification of several matrices simultaneously<nowiki>'</nowiki>
** '''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<nowiki>'</nowiki>t exist

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

Matrix derivation (analysis) - Revision history

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