A web-based comparative visualization system for human endogenous RetroVirus(HERV) on whole genomes

Abstract

Human Endogenous RetroViruses(HERVs) are suggested that they have a function of regulating the activity of human genes and could produce protein in some conditions. So it is crucial to examine the physical layout relationship between HERVs and genes in the whole genome scale. In this paper we present RetroScope, a new Web-based comparative visualization system for HERV over 4 whole primate genomes including Human, Chimpanzee, Orangutan and Rhesus monkey. So RetroScope enables us to find the retro element which is very close to a specified gene in the form of exonoverlapping or promotor, primer overlapping. Thus our system enables biologist to provide global understanding by comparing the linear configuration of several HERVs in the whole chromosome scales by using a fast HERV alignment algorithm. Also by alignment of HERVs, we can find the most similar pair of chromosomes with respect to the configuration of HERV elements, which would be another clues to construct phylogenetics based on HERV. RetroScope is available on http://neobio.cs.pusan.ac.kr/sretroscope/.