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© Oxford University Press

Methods for comparing a DNA sequence with a protein sequence

Xiaoqiu Huang and Jinhui Zhang 1

Department of Computer Science, Michigan Technological University 1400 Townsend Drive, Houghton, MI 49931
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USAE-mail: huang{at}cs.mtu.edu

We describe two methods for constructing an optimal global alignment of, and an optimal local alignment between, a DNA sequence and a protein sequence. The alignment model of the methods addresses the problems of frameshifts and introns in the DNA sequence. The methods require computer memory proportional to the sequence lengths, so they can rigorously process very huge sequences. The simplified versions of the methods were implemented as computer programs named NAP and LAP. The experimental results demonstrate that the programs are sensitive and powerful tools for finding genes by DNA-protein sequence homology.

Received on March 4, 1996; accepted on August 28, 1996

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