A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequences

In the segment-based approach to sequence alignment. nucleic acid, and protein sequence alignments are constructed from fragments, i.e., from pairs of ungapped segments of the input sequences. Given a set F of candidate fragments and a weighting function w : F + FL:, the score of an alignment is defined as the sum of weights of the fragments it consists of. and the optimization problem is to find a consistent collection of painuzse dislomt fragments wzth nmxin~um swn of wezghts. Herein, a sparse dynamic programming algorithm is described that solves the pairwise segment-alignment problem in O(L + Nmax ) space where L is the maximum length of t,he input sequences while N ,nax 5 #F holds. With a recently introduced weighting function 1~. small sets F of candidate fragments are sufficient to obtain alignments of high quality. As a result, the proposed algorithm runs in essentially linear space. @ 2001 Elsevier Science Ltd. All rights reserved Keywords-Sequence alignment, String algorithm, FYagment chaining, Dynamic programming, Complexity.