Description of algorithm

A software program MatrixScan was designed for recognition of transcription factor binding sites by trinucleotide weight matrix in arbitrary extended nucleotide sequences.

Data used in analysis

The training set of TF - sites was compiled of the sequences extracted from the database TRRD (http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd/).

The format of input data

The sequence to be analysed should have the PLAIN format and the length from 400 to 80000 bp.

How to run the program for TF - site recognition

1) Enter the sequence to be analysed into the text-box 'Sequence', If you input the sequence from file from your computer, use the dialog menu by clicking the button 'Browse'.

2) Choose the type of TF - site by selecting the option in the drop-down menu 'Type of TF - site'.

3) In case it is necessary to search for TF - sites in complementary DNA chain, click the check-box 'Reverse strand'.

4) The resulting data could be displayed in a text or graphic mode. To display the recognition function profile, click the check-box Grafic mode.

5) Click the button 'SCAN'.

6) For resetting the data, click the button 'Clear'.