MMSite – transcription factor binding sites recognition program

Pozdniakov M.A., Vityaev E.E.

1. Goal.

2. Input data description.

3. Example of site search.


1. Goal

The main goal of the program BinomSite is recognition of transcription factor binding sites in an arbitrary nucleotide sequence. The main principle of the program is scanning of the sequence to be analysed, of 30 bp in length, with the following binomial probability estimation of the regions of the sequence with each of the known transcription factor binding sites.

2. Data 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 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.

3. Example of site search.

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