Flavivirus Species Recognition Based On the Polyprotein Coding Sequences
Chaley M.B.1, Tyulko Zh.S.2, Kutyrkin V.A.3
1Institute of Mathematical Problems of Biology RAS – the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Moscow Region, Russia
2Omsk State Medical University of Ministry of Healthcare of the Russian Federation, Omsk, Russia
3Moscow State Technical University n.a. N.E. Bauman, Moscow, Russia
Abstract. Method recognizing the flavivirus species, including a subtype recognition, that based on the genome sequence analysis, is proposed. This method takes into consideration frequency characteristics of amino acid codons in the coding sequences of full-length polyprotein of flavivirus genomes. High reliability of the method is proved in recognizing flavivirus genomes from 15 groups of different species and sub-types, that are sufficiently represented in the GenBank database. Ten various species of the flaviviruses, four sub-types of Dengue virus and Kunjin virus, that is suggested to be a sub-type of West Nile virus, are considered in the work.
Key words: flavivirus genome, latent profile triplet periodicity, frequencies of amino acid codons, flavivirus species recognition.