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Nucleic Acids Research, 2003, Vol. 31, No. 13 3669-3671
© 2003 Oxford University Press

SIC: a tool to detect short inverted segments in a biological sequence

David Robelin*, Hugues Richard and Bernard Prum

Laboratoire ‘Statistique et Génome’, Tour Evry 2, 91000 Evry, France

*To whom correspondence should be addressed. Tel: +33 160 87 3808 Fax: +33 160 87 3809; Email: robelin{at}genopole.cnrs.fr

The web software SIC provides a tool to search for short inverted segments (length 3–5000 bp) in a DNA sequence. The sequence is assumed to follow a Markov model. A statistic which is sensitive to inversion is presented. Searching inverted segments is done by a scanning approach after the user specifies the size of the scanning window and the order of the Markov chain. A list of the highest score segments is given with an assessment of the randomness of the result. SIC can be accessed via the URL: http://stat.genopole.cnrs.fr/SIC/.


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