A Comparative Visualization System for the Proximity of Genes on Whole Genome Scale

Recently, increasing numbers of sense-antisense transcripts and overlapping genes have been identified in a variety of eukaryotic organisms using large-scale genome analysis. Many overlapping genes and sense-antisense transcripts have been indented in the genomes of eukaryotic, some of which have been reported to have functional roles, but their evolutionary origin is not clearly understood. We systematically analyzed all overlapping genes and sense-antisense transcripts in the eukaryotic genomes. In particular, careful comparisons were made for the othologous genes that are overlapped and sense-antisense transcripts in the various species. So we developed a evolutionary visualization tool EVOG (evolution visualizer for overlapped genes) to visualize and analyze overlapped regions from the UCSC annotation data. This tool is simple and easy to control parameters for finding overlapped genes and sense-antisense transcripts in whole genomes. In experiment we tested our system to reveal the evolutionary relation on a few related gene family. EvoG has successfully illustrated these relationship. EvoG was implemented for the component-ware design principle, which enables other people to adopt some functions easily to develop their own gene-related visualization system.