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Bioinformatics Advance Access published online on October 13, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti710
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received June 27, 2005
Revised July 13, 2005
Accepted October 6, 2005

Applications note

Suffix-Tree ANalyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes

Jacques Nicolas 1*, Patrick Durand 1, Grégory Ranchy 1, Sébastien Tempel 1, and Anne-Sophie Valin 1

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

* To whom correspondence should be addressed.
Jacques Nicolas, E-mail: stan{at}irisa.fr


  Abstract

Summary: we have developed STAN, 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 multi-part 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.


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