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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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You can use the Save list... button to export the list of matrices to a *.csv file. Later the list can be loaded from the file using the Load list... button.

The rest options are standard sequence search options: the strand and the sequence region where to search for matches.

After specifying the necessary options press the Search button. The found results will appear in the dialog table. The corresponding results identity scores are in the Score column.

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Also you can see the matrix by using the View matrix button:

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The regions found by the weight matrix algorithm can be saved as annotations to the DNA sequence in the Genbank format by pressing the Save as annotations button.

After saving, the file with resulting annotations will be automatically added to the current project, and the annotations will be added to the original sequence.

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See also:

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