COCAW: A Genome-wide Pattern Search System for Designing Microbial Probes.

Ryu,  Seunghee; Park,  Kiejung; Lee,  Dohoon; Kim,  Cheol Min

doi:2009.7.3.178

Genomics Inform > Volume 7(3); 2009 > Article

Note

Genomics & Informatics 2009;7(3): 178-180.

DOI: https://doi.org/10.5808/gi.2009.7.3.178

COCAW: A Genome-wide Pattern Search System for Designing Microbial Probes.

Seunghee Ryu, Kiejung Park, Dohoon Lee, Cheol Min Kim

¹Visual and Biomedical Computing Lab., Pusan National University, Busan 609-735, Korea.
²PNU SuperComputing Center, Pusan National University, Busan 609-735, Korea.
³Information Technology Institute, SmallSoft Co. Ltd., Daejeon 305-343, Korea.
⁴School of Medicine, Pusan National University, Busan 609-735, Korea. kimcm@pusan.ac.kr

Abstract

A few bioinformatics tools have been used to find out conserved regions as probes. We have developed a system based on a heuristic method with web interfaces to find out conserved regions against microbial genomes. The system runs in real time by using relative entropy in limited narrow regions and detecting similar regions between pair regions with local alignment. The system could be useful to find out conserved regions as genome-wide scale.

Keywords: genome project; genome-wide search; primer design; probe design