A FPGA based coprocessor for gene finding using Interpolated Markov Model (IMM)

Author

Chrysos, G. ; Sotiriades, E. ; Papaefstathiou, I. ; Dollas, A.

Author_Institution

Dept. of Electron. & Comput. Eng., Tech. Univ. of Crete, Chania, Greece

fYear

2009

fDate

Aug. 31 2009-Sept. 2 2009

Firstpage

683

Lastpage

686

Abstract

An important biology problem is the decoding of the DNA and the extraction of useful genetic information. There are many bioinformatics algorithms that try to solve the gene finding problem and one of the most efficient is the Glimmer algorithm. In this paper, we present a hardware architecture that implements the Glimmer algorithm. The architecture was developed specifically for the capabilities of present-day FPGAs. In addition, this paper presents an efficient hardware method to construct a huge but very sparse lookup table by taking advantage the tree-like structure of memories.

Keywords

DNA; Markov processes; bioinformatics; coprocessors; field programmable gate arrays; genetics; interpolation; table lookup; tree data structures; DNA decoding; FPGA-based coprocessor; Glimmer algorithm; IMM; bioinformatics algorithm; biology problem; gene finding problem; gene identification; genetic information extraction; hardware architecture; interpolated Markov model; sparse lookup table; tree-like memory structure; Bioinformatics; Biological system modeling; Coprocessors; DNA; Data mining; Decoding; Field programmable gate arrays; Genetics; Hardware; Table lookup;

fLanguage

English

Publisher

ieee

Conference_Titel

Field Programmable Logic and Applications, 2009. FPL 2009. International Conference on

Conference_Location

Prague

ISSN

1946-1488

Print_ISBN

978-1-4244-3892-1

Type

conf

DOI

10.1109/FPL.2009.5272367

Filename

5272367