A greedy algorithm for aligning DNA sequences - PubMed (original) (raw)
A greedy algorithm for aligning DNA sequences
Z Zhang et al. J Comput Biol. 2000 Feb-Apr.
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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