Jornal de Bioinformática Aplicada e Biologia Computacional

Testing the Metagenome Composition by the Method of Sequential Set of Primers

Valery Kirzhner, Zeev Volkovich, Renata Avros and Elena Ravve

Metagenome is a mixture of different genomes and the analysis of its composition is, currently, a challenging problem of bioinformatics. In the present study, we attempt to solve this problem using DNAmarker primers-short nucleic acid fragments. Formally speaking, each primer maps a genome into a finite set of integral numbers. This set is called the genome spectrum for the given primer and is unique for each genome. The union of the genetic material of two genomes is mapped into the union of their spectra. Thus the metagenome spectrum always includes (covers) the spectra of the constituting genomes. A genome whose spectrum is not covered by the metagenome one, cannot be part of the metagenome, while the spectrum of a genome that is not included in the metagenome can accidentally be covered by the metagenome spectrum. However, if covering occurs for a few different primers, the probability of the genome inclusion in the metagenome can be estimated, the accuracy depending on the number of the primers used. In the present study, the estimations are made for the case of random primers and their effectiveness is assessed using the computer simulation of the RAPD technology.