Computer system for investigating the properties of mobile genetic elements

At present it has been established that eukariotic genomes contain a considerable number of mobile genetic elements (MGE). Such sequences are an essential factor of evolution and functioning of genomes affecting organism fitness. The present paper is devoted to description of computer methods for studying MGE properties aggregated within a complex of programs IBM PC computer. Section 2 describes the methods for estimating MGE transposition parameters. Firstly, there is a method for a mathematical simulation of evolutionary dynamics of MGE number in genome, using experimental information on flanking direct short repeats. As a result one can obtain estimates of both the replicative transposition frequency lambda and that of MGE excision from the genome mu. Secondly (Section 2.2), there is a method for imitation simulation of MGE evolution in the genome permitting one apart from obtaining the estimates of frequencies lambda and mu to obtain those of accurate determination of lambda and mu depending on experimental data volume. Finally, in Section 2.3 we describe a method for evaluating transposition frequency values using phylogenetic analysis. All three methods provide identical estimates and are complementary. In Section 3.1 pseudoclusters method is described which makes is possible to estimate efficiency of exchange processes (those of gene conversion and unequal crossingover) with taking part of clustered MGE. This method made it possible to show that in clusters of Alu repeats the exchange processes can proceed between the oppositly-oriented repeats. Section 3.2 contains a description of a method for estimating the frequency of unequal crossingover, based on analysis (using imitation simulation) of redistributing direct short flanking repeats in MGE clusters. In Section 3.3 we present a method for revealing the effect of gene conversion. We managed to show their manifestation for Alu repeats in the human genome. Section 4 describes a method for evaluating the influence of MGE transposition on fitness, based on calculation of genetic load value in the population. Finally, Section 5 provides data base for structural-functional MGE organization, that is designed for a joint detailed analysis of MGE properties by various methods within the frameworks of a common complex of program.