View source for Continue CMA (analysis)

;Analysis title
:[[File:Composite-module-analyses-Continue-CMA-icon.png]] Continue CMA
;Provider
:[[geneXplain GmbH]]
;Class
:{{Class|biouml.plugins.cma.analysis.CMAFurtherRunner}}
;Plugin
:[[Biouml.plugins.cma (plugin)|biouml.plugins.cma (Composite module analyst)]]

==== Description ====
Run CMA starting with best model of input result.

==== Parameters: ====

* '''CMA result''' – Result of the construct composite modules analysis
* '''Genetic algorithm parameters''' (expert) – Genetic algorithm parameters
** '''Number of iterations''' – Number of iterations
** '''Population size''' – Population size
** '''Non-change limit''' – Number of iterations to stop after if best score is not improved
** '''Elite size''' – Number of elite organisms (i.e. best organisms to survive unconditionally)
** '''Mutation rate''' – This controls how often mutation occurs and how significant they are (0..1)
* '''Score calculation parameters''' (expert) – Parameters which control score calculation
** '''Penalty rate''' – Which penalty value will be assigned
** '''Site models in focus''' – At least one of these models must present in the resulting composite model to have non-zero score
** '''Site models in focus table''' (expert) – The table of site models in focus
** '''All modules contain site model in focus''' – If checked, then each module must contain at least one site model from the focus
** '''Focused sequences percent''' – Minimal percent of sequences in yes-set which actually contains sites of site models in focus
** '''Sequence column''' – Column to take sequences from
** '''Sequences in focus''' – Selected sequences should be in the result top
** '''Top sequences size (percent)''' – Size of sequences (in percent) that will be considered as top
** '''Sequences in focus in top (percent)''' – Minimal percent of sequences in focus in the top
* '''Model parameters''' – Model parameters
** '''Min modules''' – Minimal number of modules
** '''Max modules''' – Maximal number of modules
** '''Gaussian model''' (expert) – Gaussian model
*** '''Min models''' – Minimal number of site models in module
*** '''Max models''' – Maximal number of site models in module
*** '''Min sites to account''' – Minimal number of sites to account
*** '''Max sites to account''' – Maximal number of sites to account
*** '''Min module width''' – Minimal width (sigma) of the module
*** '''Max module width''' – Maximal width (sigma) of the module
*** '''Pairs mode''' – Whether the sites of at least two different site models satisfying the cut-off condition must be present on the sequence
* '''Output path''' – Path to analysis result

[[Category:Analyses]]
[[Category:Composite module analyses (analyses group)]]
[[Category:GeneXplain analyses]]
[[Category:Autogenerated pages]]