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) × (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.