Detecting periodic patterns in biological sequences.

  • Coward E
  • Drablos F
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Abstract

Motivation: The search for repeated patterns in DNA and
protein sequences in important in sequence analysis. The
rapid increase in available sequences, in particular from
large-scale genome sequencing projects, makes it relevant
to develop sensitive automatic methods for the
identification of repeats. Results: A new method for
finding periodic patterns in biological sequences is
presented. The method is based on evolutionary distance and
'phase shifts' corresponding to insertions and deletions. A
given sequence is aligned to itself in a certain sense,
trying to minimize a distance to periodicity. Relationships
between different such periodicity measures are discussed.
An iterative algorithm is used, and the running time is
nearly proportional to the sequence length. The alignment
produces a periodic consensus pattern. A 'phase score' is
used to indicate a statistical significance of the
periodicity. Three examples using both DNA and protein
sequences illustrates how the method can be used to find
patterns.

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Authors

  • E Coward

  • F Drablos

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