  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.
