A software program ARGO_Viewer was designed for recognition of regulatory gene regions in arbitrary extended nucleotide sequences.
2. Brief description of the method
Promoters are recognised in extended genome regions by estimating the set R of region-specific motifs found by the program ARGO. A window of 400 bp in length, corresponding to promoter region [-300;+100], slides with the interval of 10 bp along the sequence analysed. For each position of this window, the recognition potential is evaluated at this region of the sequence analysed. By these recognition potentials, a profile of recognition function is constructed. Positions of the window with recognition function values exceeding 0 mark potential transcription start sites.
The method is based on the following idea. At the first stage, by analysing each promoter sequence from the training set, all specific motifs are found in the set. For promoter recognition in an arbitrary sequence, the program determines its specific oligonucleotide motifs and compares them with the analogous motifs in the training set of promoter sequences. If in the training set there exists a promoter characterised by the pattern of motif distribution statistically similar to that in the sequence analysed, then the solution is made that the sequence under study contains a promoter.
3. Data used in analysis
The training set of promoters was compiled of the sequences extracted from the database TRRD (http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd/).
4. The format of input data
The sequence to be analysed should have the PLAIN format and the length from 400 to 80000 bp.
5. How to run the program for promoter 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 promoter by selecting the option in the drop-down menu ‘Type of promoter’.
3) In case it is necessary to search for promoters 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’.