MMSite – transcription factor binding sites recognition program

Pozdniakov M.A., Vitaev E.E.

1. Goal.

2. Theoretical model and data representation.

3. Input data description.

4. Example of site search.

5. References.


1. Goal

The goal of the program MMSite is recognition of transcription factor binding sites in an arbitrary nucleotide sequence. Method used in the program is based on the multidimensional alignment of query sequence parts with the set of known site sequences. Multidimensional alignment is a new method of site search. The program analyses such alignment by four methods described below. There is possibility to output the results of the program execution by a single chosen method or by a combination of these methods. Also for each transcription factor, the program may automatically choose the optimal recognition method.

2. Theoretical model and data representation.

The program performs the search for transcription factor binding sites by using four methods:

Multidimensional alignment with theset of known sites;

Pair alignment of query sequence fragment with the single known site, which is most similar to it;

Weight matrices;

Information content.

Sets of transcription factor binding sites were extracted from the TRRD database.

3. Input, and output description.

Enter your nucleotide sequence into the text-box from clipboard or from file by using the dialog menu ‘Browse’. The sequence should be in the FASTA format and contain only the symbols a,c,t,g,A,C,T,G.

Choose the name of transcription factor in the drop-down menu with the list of transcription factors.

Choose the recognition method or set of methods that will be applied for site searching or choose the option ‘optimal method’, if you want the program to detect the optimal method automatically. Optimal method discriminates sites from random sequences better than the other methods available.

Choose significance level in the drop-down menu ‘Threshold’.

Choose direction of your sequence by clicking the check-box ‘Reverse strand’. If this button is not clicked, the search will be done directly in your sequence, otherwise in complementary strand.

Choose the form of output data representation, textual or graphical mode.

Click the button ‘Scan’ and wait for the end of the program execution.

4. Example of site search.

Click the button ‘Example’ to display the example of the program execution.


5. References.

[1] Comparative analysis of transcription factor recognition methods

Pozdniakov M.A., Vityaev E.E., Ananko E.A., Ignatieva E.V., Podkolodnaya O.A., Podkolodny N.L., Lavrushev S.V.,Kolchanov N.A.// Molecular biology, in press (in Russia)