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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, andand UniPROBE containing weight matrices.
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To search for transcription factor binding sites in a DNA sequence select the Analyze ‣ Search TFBS with matrices... context menu item. The Weight matrix search dialog will appear:
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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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