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Nucleic Acids Research, 1983, Vol. 11, No. 13 4629-4634
© 1983

MOLECULAR BIOLOGY

An efficient method for finding repeats in molecular sequences

Hugo M. Martinez

Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA

Received April 4, 1983. Revised May 23, 1983. Accepted May 31, 1983.

The problem of finding repeats in molecular sequences is approached as a sorting problem. It leads to a method which is linear in space complexity and NlogN in expected time complexity. The implementation is straightforward and can therefore be used to handle large sequences with relative ease. Of particular interest is that several sequences can be treated as a single sequence. This leads to an efficient method for finding dyads and for finding common features of many sequences, such as favorable alignments.


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