The Weight Matrix plugin is a tool for solving the problem of a sequence annotating. As well as for the SITECON, the main use case of the plugin is recognition of potential transcription factor binding sites on basis of the data about conservative conformational and physicochemical properties revealed with the binding sites sets analysis.
The Weight Matrix contains a lot of position frequency matrices (PFM ‘s) and position weight matrices (PWM ‘s, also known as position specific score matrices — PSSM ‘s). The matrices came from two wide-known open archives: JASPAR, which contains frequency matrices, andUniPROBE containing weight matrices.
Also the Weight Matrix plugin provides a tool for creating specific position frequency and weight matrices from an existing alignment or from a file with several sequences. The created matrix can be used as a profile for the search as well as the JASPAR and UNIPROBE ones.
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In the search dialog you must specify a file with PWM or PFM. You can do so by pressing the browse button [1] and selecting the file.
Also you can use the special interface to choose a JASPAR matrix by pressing the Search JASPAR database button [2].
Alternative way to specify the position weight/frequency matrix is to create a specific one from an alignment or a file with several sequences with the build a new matrix tool.
After the profile (the matrix) is loaded, you can adjust the threshold value [3]. The threshold sets the minimal identity score for a result to pass. The more the result score is, the more it is homologically related to the aligned region. By changing the threshold you can filter low- scoring results.
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