A greedy algorithm for aligning DNA sequences

J Comput Biol. 2000 Feb-Apr;7(1-2):203-14. doi: 10.1089/10665270050081478.


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.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms*
  • Biometry
  • DNA / genetics*
  • Databases, Factual
  • Sequence Alignment / statistics & numerical data*
  • Sequence Analysis, DNA / statistics & numerical data
  • Software


  • DNA