Title :
Development of new method of primer design based on Genomewide for SNP typing under problem solving environment on grid
Author :
Oroguchi, T. ; Inoue, Tomofumi ; Tomabechi, Isao ; Tago, Yoshio ; Makino, Toru
Author_Institution :
Div. of Math. & Inf. Sci., Kanazawa Univ.
Abstract :
How primers are specific to target base sequences containing single nucleotide polymorphism (SNP) is considered as the key to SNP analysis. In this study, we have attempt to develop a high-accuracy primer design. For that purpose, we have developed problem solving environment (PSE) on grid system and established an environment to execute Basic Local Alignment Search Tool (BLAST) genome-widely. We have applied this primer design system in the PSE to drug-metabolizing enzyme and verified that this new design method generated highly accurate primers compared with the existing methods by means of computation and experiment. We have also developed a work/low system for the PSE on the grid system and achieved remarkable improvement in efficiency of the primer design. The new method have achieved more than 10 times efficiency compared with the existing methods
Keywords :
biology computing; drugs; enzymes; grid computing; pharmaceutical technology; BLAST; Basic Local Alignment Search Tool; Genomewide; base sequences; drug-metabolizing enzyme; grid computing; grid system; primer design; problem solving environment; single nucleotide polymorphism typing; Bioinformatics; Constitution; DNA; Design methodology; Drugs; Genomics; Information analysis; Pharmaceutical technology; Problem-solving; Sequences;
Conference_Titel :
e-Science and Grid Computing, 2005. First International Conference on
Conference_Location :
Melbourne, Vic.
Print_ISBN :
0-7695-2448-6
DOI :
10.1109/E-SCIENCE.2005.31
