Difference between revisions of "Site model (element type)"

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{{Element type|site model|ru.biosoft.bsa.SiteModel}}
 
{{Element type|site model|ru.biosoft.bsa.SiteModel}}
 
=== Description ===
 
=== Description ===
[[File:Type-site-model-info-box-web.png|thumb|Site model selected in the tree with its description in the [[information box]].]]Site model is the mathematical model of [[:wikipedia:DNA binding site|DNA binding site]] (motif). There are several kinds of site models which differ in algorithm of determination whether given sequence should be considered as predicted motif or not. Usually site model is based on one or more {{Type link|matrix|weight matrices}} and one or more threshold (cut-off) values. Cutoff values can be changed using [[Change profile cutoffs (analysis)|Change profile cutoffs]] analysis.
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[[File:Type-site-model-info-box-web.png|thumb|Site model selected in the tree with its description in the [[information box]].]]Site model is the mathematical model of [[:wikipedia:DNA binding site|DNA binding site]] (motif). There are several kinds of site models which differ in algorithm of determination whether given sequence should be considered as predicted motif or not. Usually site model is based on one or more {{Type link|matrix|weight matrices}} and one or more threshold (cut-off) values. Cut-off values can be changed using [[Change profile cutoffs (analysis)|Change profile cutoffs]] analysis.
  
 
Predefined site models come with databases like [[GTRD]]. Some analysis methods like [[Create weight matrix model (analysis)|Create weight matrix model]] may create new site models. The primary usage for site models is [[Site search on track (analysis)|Site search on track]] and [[Site search on gene set (analysis)|Site search on gene set]] analyses.
 
Predefined site models come with databases like [[GTRD]]. Some analysis methods like [[Create weight matrix model (analysis)|Create weight matrix model]] may create new site models. The primary usage for site models is [[Site search on track (analysis)|Site search on track]] and [[Site search on gene set (analysis)|Site search on gene set]] analyses.

Latest revision as of 17:15, 17 May 2013

Title
Type-site-model-icon.png site model
Class
SiteModel

[edit] Description

Site model selected in the tree with its description in the information box.
Site model is the mathematical model of DNA binding site (motif). There are several kinds of site models which differ in algorithm of determination whether given sequence should be considered as predicted motif or not. Usually site model is based on one or more Type-matrix-icon.png weight matrices and one or more threshold (cut-off) values. Cut-off values can be changed using Change profile cutoffs analysis.

Predefined site models come with databases like GTRD. Some analysis methods like Create weight matrix model may create new site models. The primary usage for site models is Site search on track and Site search on gene set analyses.

Site models can only reside in Type-profile-icon.png profiles.

Site models cannot be opened as documents. However when you select the site model in the tree, you can read the comprehend description in the information box.

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