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JCB
2000

A Greedy Algorithm for Aligning DNA Sequences

13 years 3 months ago
A Greedy Algorithm for Aligning DNA Sequences
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. Key words: sequence alignment, greedy algorithms, dynamic programming.
Zheng Zhang 0004, Scott Schwartz, Lukas Wagner, We
Added 18 Dec 2010
Updated 18 Dec 2010
Type Journal
Year 2000
Where JCB
Authors Zheng Zhang 0004, Scott Schwartz, Lukas Wagner, Webb Miller
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