Analysis of Metagenome Composition by the Method of Random Primers

Metagenome, a mixture of different genomes (as a rule, bacterial), represents a pattern, and the analysis of its composition is, currently, one of the challenging problems of bioinformatics. In the present study, the possibility of evaluating metagenome composition by DNA-marker methods is investigated. These methods are based on using primers, short nucleic acid fragments. Each primer picks out of the tested genome the fragment set specific just for this genome, which is called its spectrum (for the given primer) and is used for identifying the genome. The DNA-marker method, applied to a metagenome, also gives its spectrum, which, obviously, represents the union of the spectra of all genomes belonging to the metagenome. Thus each primer provides a projection of the genomes and of the metagenome onto the corresponding spectra set. Here we propose to apply the random projection (random primer) approach for analyzing metagenome composition and present some estimates of the method effectiveness for the case of Random Amplified Polymorphic DNA (RAPD) technology.