### Occurrence probability of
structured motifs in random sequences

####
**Stéphane Robin, Jean-Jacques Daudin, Hughes Richard, Marie-France
Sagot and Sophie Schbath**

*Journal of Computational Biology*,
9:761-773, 2002

The problem of extracting from a set of nucleic acid sequences motifs
which may have biological function is more and more important. In this
paper, we are interested in particular motifs that may be implicated
in the transcription process. These motifs, called structured motifs,
are composed of two ordered parts separated by a variable distance and
allowing for substitutions. In order to assess their statistical
significance, we propose approximations of the probability of
occurrences of such a structured motif in a given sequence. An
application of our method to evaluate candidate promoters in
*E. coli* and *B. subtilis* is presented. Simulations show
the goodness of the approximations

**key words:** Markov models, motif occurrencess, promoters,
structured motifs

Paper in postscript format

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