论文信息 - Whole Genome Alignment with BLAST on Grid Environment

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.

[1] S. Salzberg,et al. Alignment of whole genomes. , 1999, Nucleic acids research.

[2] Richard J. Mural,et al. Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs , 2005, Bioinform..

[3] Lukas Wagner,et al. A Greedy Algorithm for Aligning DNA Sequences , 2000, J. Comput. Biol..

[4] Hongyu Zhang,et al. Alignment of BLAST High-scoring Segment Pairs Based on the Longest Increasing Subsequence Algorithm , 2003, Bioinform..

[5] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.

[6] J. Jurka. Repbase update: a database and an electronic journal of repetitive elements. , 2000, Trends in genetics : TIG.

[7] D. Haussler,et al. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[8] W. J. Kent,et al. BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[9] D. Haussler,et al. Human-mouse alignments with BLASTZ. , 2003, Genome research.