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A greedy algorithm for aligning DNA sequences (2000)
| Venue: | J. COMPUT. BIOL |
| Citations: | 572 - 16 self |
BibTeX
@ARTICLE{Zhang00agreedy,
author = {Zheng Zhang and Scott Schwartz and Lukas Wagner and Webb Miller},
title = {A greedy algorithm for aligning DNA sequences},
journal = {J. COMPUT. BIOL},
year = {2000},
volume = {7},
number = {1},
pages = {203--214}
}
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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.
