The computer system of functional sites' analysis in polinucleotide sequences

The present paper is devoted to description of a computer system for functional sites analysis in polynucleotide sequences. This system searches for different types of characteristics in oligonucleotides and repeats distribution in functional sites. Significance of revealed characteristics is estimated by the complex of statistic analysis programmes. Out of a great number of characteristics the set of most valuable ones is chosen. On their basis the search for functional sites of a certain type in nucleotide sequences in possible. The system consists of several programed blocks. 1) Block of controlling the process of characteristics search. 2) Block of characteristics calculations. 3) Block of statistical analysis. 4) Block of the initial interpretation of results. In Fig.2 block-scheme of the whole system is presented. In the present system three strategies of valuable characteristics search are realized: 1) Analysis of different types of repeat in nucleotide sequences. 2) Analysis of oligonucleotides frequency of different length. 3) Analysis preferable localization of separate nucleotide groups in different positions of four nucleotide length subsequences. Statistical analysis is carried out by calculating the utility of a given characteristics at classification of functional sites of the present type. The description of the block of statistic analysis is given in section 2. Characteristics value showing the presence of repeats is calculated by the formulas (2) and (3). Characteristics value of showing oligonucleotide frequencies are calculated by formulas (4) and (5). Two functional sites samplings are analysed by the worked out system: 1) promoters of E. coli, some phages and plasmids, 2) initiation translation sites. In these functional sites informatively-valuable repetitions and oligonucleotides of a certain type dispersed on the whole sequence length were found. In Fig. 8 hypothetic mechanism of the found oligonucleotide participation in promoters functioning (in the process of the open complex forming) is shown. The worked out system of searching for regularities in functional sites is a subsystem of an expert system for functional sites analysis in nucleotide sequences. The general scheme of this expert system is given in Fig. 10.