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Bioinformatics Advance Access originally published online on October 13, 2005
Bioinformatics 2005 21(24):4408-4410; doi:10.1093/bioinformatics/bti710
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Suffix-tree analyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes

Jacques Nicolas *, Patrick Durand , Grégory Ranchy , Sébastien Tempel and Anne-Sophie Valin

IRISA-INRIA, Campus de Beaulieu 35402 Rennes cedex, France

*To whom correspondence should be addressed.

Summary: We have developed STAN (suffix-tree analyser), a tool to search for nucleotidic and peptidic patterns within whole chromosomes. Pattern syntax uses a string variable grammar-like formalism which allows the description of complex patterns including ambiguities, insertions/deletions, gaps, repeats and palindromes. STAN is based on a reduction to multipart matching on a suffix-tree data structure and can handle large DNA sequences, whether assembled or not.

Availability: STAN is accessible online at http://www.irisa.fr/symbiose/STAN

Contact: stan{at}irisa.fr

Received on June 27, 2005; revised on July 13, 2005; accepted on October 6, 2005

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