Space-Conserving Optimal DNA-Protein Alignment

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)

• Type: Conference
• Year: 2004
• Where: CSB
• Authors: Pang Ko, Mahesh Narayanan, Anantharaman Kalyanaraman, Srinivas Aluru
• Keywords: Bioinformatics, Coding Sequences, CSB 2004, DNA-protein Alignment, DNA-protein Alignment Algorithms