An exact formula for the number of alignments between two DNA sequences

DNA Seq. 2003 Dec;14(6):427-30. doi: 10.1080/10425170310001617894.


Given two DNA sequences, one is usually interested in measuring their similarity. For this purpose we have to consider different alignments of both the sequences. The number of alignments grows rapidly with the length of the sequences. In this short communication, we give an exact formula for the number of possible alignments using the theory of difference equations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Base Sequence*
  • Models, Theoretical
  • Sequence Alignment / methods*