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, 7 (1-2), 203-14

A Greedy Algorithm for Aligning DNA Sequences

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A Greedy Algorithm for Aligning DNA Sequences

Z Zhang et al. J Comput Biol.

Abstract

For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy alignment algorithm with particularly good performance and show that it computes the same alignment as does a certain dynamic programming algorithm, while executing over 10 times faster on appropriate data. An implementation of this algorithm is currently used in a program that assembles the UniGene database at the National Center for Biotechnology Information.

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