Space-conserving optimal DNA-protein alignment.

Pang Ko; Mahesh Narayanan; Anantharaman Kalyanaraman; Srinivas Aluru

doi:10.1109/csb.2004.1332420

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Space-conserving optimal DNA-protein alignment.

Pang Ko·Mahesh Narayanan·Anantharaman Kalyanaraman·Srinivas Aluru

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Abstract

DNA-protein alignment algorithms can be used to discover coding sequences in a genomic sequence, if the corresponding protein derivatives are known. They can also be used to identify potential coding sequences of a newly sequenced genome, by using proteins from related species. Previously known algorithms either solve a simplified formulation, or sacrifice optimality to achieve practical implementation. In this paper, we present a comprehensive formulation of the DNA-protein alignment problem, and an algorithm to compute the optimal alignment in O(mn) time using only four tables of size (m + 1) x (n + 1), where m and n are the lengths of the DNA and protein sequences, respectively. We also developed a Protein and DNA Alignment program PanDA that implements the proposed solution. Experimental results indicate that our algorithm produces high quality alignments.

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Algorithms Base Sequence DNA Data Compression Molecular Sequence Data Proteins Sequence Alignment Sequence Analysis, DNA Sequence Analysis, Protein Evaluation Study Journal Article Research Support, U.S. Gov't, Non-P.H.S.

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Pang Ko, Mahesh Narayanan, Anantharaman Kalyanaraman, Srinivas Aluru. 2004. Space-conserving optimal DNA-protein alignment.. https://doi.org/10.1109/csb.2004.1332420

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