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PubMed · 10890397

A greedy algorithm for aligning DNA sequences.

Z Zhang·S Schwartz·L Wagner·W Miller
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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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AlgorithmsBiometryDNADatabases, FactualSequence AlignmentSequence Analysis, DNASoftwareJournal ArticleResearch Support, U.S. Gov't, P.H.S.

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Z Zhang, S Schwartz, L Wagner, W Miller. A greedy algorithm for aligning DNA sequences.. https://doi.org/10.1089/10665270050081478

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