Whole Genome Alignment with BLAST on Grid Environment

BLAST is a widely used sequence alignment tool for comparing the similarity of DNA and protein. However, it is not commonly used in whole genome alignment because of its computational cost. We could solve the computational problem by using fragmentation based alignment on computing grid environment. The BLAST based genome alignment was sensitive in target sequence finding and flexible for the processing of alignment results. Therefore, various procedures could be tested to get more accurate whole genome alignment. The approach is used to align whole human chromosomes and mouse chromosomes. Compared to other genome alignment methods, we could get alignment list matched well with known synteny map data within reasonable time.