Toward Chromosome-Level Comparative Analysis of Vertebrate Genomes

Abstract

Since the publication of the human draft genome sequence, steady progress around the world is made to analyze the genome. In addition, mouse genome project and other vertebrate genome projects of model organisms are rapidly producing much genomic sequences. Comparative analysis is becoming increasingly important as a tool for genome sequence analysis [3]. In this study, we focus on vertebrate genome sequences of various species, such as human, mouse and rat. The evolutionary conserved regions in human genome sequences are identified effectively by the comparison with those vertebrate genome sequences. The main goal of this research is to identify novel genes and regulatory regions and to elucidate genome-level events in evolution from genome sequences. We have developed a comparative genome system which collects data, compares them, visualizes the results, and produces primer sets using primer3 [6] for the PCR experiments for confirmation of the exon prediction. Users can submit syntenic genomic sequences or select a publicly available syntenic region. The system allow the users to analyze and convert data easily, so that users can browse the various analysis results using PipMaker [4] (WWW server for genome comparison and java application laj), and Alfresco [2] (java application), without producing annotation files on their own.