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Nucleic Acids Research, 2003, Vol. 31, No. 13 3679-3681
© 2003 Oxford University Press

SPA: simple web tool to assess statistical significance of DNA patterns

H. Richard and G. Nuel*

Laboratoire Statistique et Genome, CNRS, INRA, Genopole, Université d'Evry Val d'Essone, 523 place des terrasses, 91000 Evry, France

*To whom correspondence should be addressed. Tel: +33 1 60 87 88 01; Fax: +33 1 60 87 38 09; Email: nuel{at}genopole.cnrs.fr

Many statistical methods and programs are available to compute the significance of a given DNA pattern in a genome sequence. In this paper, after outlining the mathematical background of this problem, we present SPA (Statistic for PAtterns), an expert system with a simple web interface designed to be applied to two of these methods (large deviation approximations and exact computations using simple recurrences). A few results are presented, leading to a comparison between the two methods and to a simple decision rule in the choice of that to be used. Finally, future developments of SPA are discussed. This tool is available at the following address: http://stat.genopole.cnrs.fr/SPA/.


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