Design and implementation of parallel algorithms for gene-finding

Author

Puthukattukaran, James ; Chalasani, Suresh ; Senapathy, Periannan

Author_Institution

Dept. of Electr. & Comput. Eng., Wisconsin Univ., Madison, WI, USA

fYear

1994

fDate

2-5 Aug 1994

Firstpage

186

Lastpage

193

Abstract

Finding genes unequivocally in DNA sequences is one of the key goals of the Human Genome project. The human genome is a 3 billion character long DNA sequence and is estimated to contain about 100000 genes. It has been shown by several biologists that genes in a DNA sequence satisfy certain special properties. We use a combination of these properties to design a serial algorithm for gene-finding. To speed up the process of finding genes in long DNA sequences (of the order of ⩾100000 characters), we design a parallel algorithm for gene-finding. We have implemented the parallel gene-finding algorithm on the CM-5 multicomputer as well as on a network of HP Apollo workstations under Parallel Virtual Machine software package. Experimental results indicate that our algorithms predict genes with reasonable accuracy

Keywords

DNA; biology computing; cellular biophysics; parallel algorithms; parallel machines; CM-5 multicomputer; DNA sequences; HP Apollo workstations; Human Genome project; PVM; Parallel Virtual Machine; gene-finding; parallel algorithm; parallel algorithm design; parallel gene-finding algorithm; serial algorithm; software package; Algorithm design and analysis; Bioinformatics; DNA; Genomics; Humans; Parallel algorithms; Sequences; Software algorithms; Virtual machining; Workstations;

fLanguage

English

Publisher

ieee

Conference_Titel

High Performance Distributed Computing, 1994., Proceedings of the Third IEEE International Symposium on

Conference_Location

San Francisco, CA

Print_ISBN

0-8186-6395-2

Type

conf

DOI

10.1109/HPDC.1994.340245

Filename

340245