Site model (element type)

Title

site model

Class

SiteModel

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 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 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.