期刊
JOURNAL OF COMPUTATIONAL BIOLOGY
卷 7, 期 1-2, 页码 203-214出版社
MARY ANN LIEBERT INC PUBL
DOI: 10.1089/10665270050081478
关键词
sequence alignment; greedy algorithms; dynamic programming
类别
资金
- NLM NIH HHS [LM05110] Funding Source: Medline
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 Set produce an alignment that is guaranteed to be theoretically optimal. We introduce a nem 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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