Comparison of Genomes Using High-Performance Parallel Computing

Comparison of the DNA sequences and genes of two genomes can be useful to investigate the common functionalities of the corresponding organisms and get a better understanding of how the genes or groups of genes are organized and involved in several functions. In this paper we use high-performance parallel computing to compare the whole genomes of two organisms, namely Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris, each with more than five million basepairs. Our purpose is two-fold. First we intend to exploit the high-performance power of a cluster of low-cost microcomputers, propose a parallel solution to this problem, and show its feasibility with implementation and performance results. Second we do additional comparisons of the two genomes by locating and compare not only the homologous genes (expressed in terms of the 20-letter amino acids) but also compare the regions or gaps (in terms of the 4letter DNA nucleotides) between the corresponding homologo...

• Type: Conference
• Year: 2003
• Where: sbacpad
• Authors: Nalvo F. Almeida Jr., Carlos E. R. Alves, Edson Cáceres, Siang W. Song
• Keywords: Computer Architecture, Hardware, Homologous Genes, SBACPAD 2003, Xanthomonas Axonopodis Pv, Xanthomonas Campestris