Comparative Analysis on the Conservation of Two Orthologous Genome Regions

Abstract

Recently, draft sequences of human and mouse genome have been released. Such genomic sequence data are increasing very rapidly and effective annotation methods are required. Investigating orthologous contigs of two genomes can be very useful to understand their functional similarities and differences. Especially, as the mouse becomes a leading model for studying disease processes in humans, the emerging mouse genome data have become valuable resources for functional studies [1]. So far there have been several approaches to analyze important CDS (coding sequence) regions and non-CDS (e.g. promoter, polyA, etc.) regions individually. Here, we tried to systemically analyze coding and non-coding human and mouse orthologous regions with putative annotations by several prediction tools (e.g. Genscan, RepeatMasker, Sim4, etc.) accompanying database search (TIGR Gene Indices [7]) as well as with known annotations extracted from Genbank flat data files. Finally web-based visualization tools were applied to display comparative genomic information effectively.