A run-time reconfigurable system for gene-sequence searching

Author

Puttegowda, Kiran ; Worek, William ; Pappas, Nicholas ; Dandapani, Anusha ; Athanas, Peter ; Dickerman, Allan

Author_Institution

Virginia Polytech. Inst. & State Univ., Blacksburg, VA, USA

fYear

2003

fDate

4-8 Jan. 2003

Firstpage

561

Lastpage

566

Abstract

Advances in the field of bio-technology has led to an ever increasing demand for computational resources to rapidly search large databases of genetic information. Databases with billions of data elements are routinely compared and searched for matching and near-matching patterns. We present a system developed to search DNA sequence data using run-time reconfiguration of field programmable gate arrays (FPGAs). The system provides an order of magnitude increase in performance while reducing hardware complexity when compared to existing commercial systems.

Keywords

DNA; biological techniques; biotechnology; field programmable gate arrays; genetics; information resources; molecular biophysics; DNA sequence data; bio-technology; computational resources; data elements; databases; field programmable gate arrays; gene-sequence searching; genetic information; hardware complexity; near-matching patterns; run-time reconfigurable system; run-time reconfiguration; Bioinformatics; Costs; DNA; Databases; Field programmable gate arrays; Genetics; Hardware; Proteins; Runtime; Sequences;

fLanguage

English

Publisher

ieee

Conference_Titel

VLSI Design, 2003. Proceedings. 16th International Conference on

ISSN

1063-9667

Print_ISBN

0-7695-1868-0

Type

conf

DOI

10.1109/ICVD.2003.1183193

Filename

1183193