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Bioinformatics Advance Access originally published online on May 16, 2008
Bioinformatics 2008 24(13):1536-1537; doi:10.1093/bioinformatics/btn234
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Swelfe: a detector of internal repeats in sequences and structures

Anne-Laure Abraham 1,2,*, Eduardo P. C. Rocha 1,2 and Joël Pothier 1

1UPMC Univ Paris 06, Atelier de BioInformatique, F75005 Paris and 2Institut Pasteur, Microbial Evolutionary Genomics; CNRS, URA2171, F75015 Paris, France

*To whom correspondence should be addressed.


  Abstract

Summary: Intragenic duplications of genetic material have important biological roles because of their protein sequence and structural consequences. We developed Swelfe to find internal repeats at three levels. Swelfe quickly identifies statistically significant internal repeats in DNA and amino acid sequences and in 3D structures using dynamic programming. The associated web server also shows the relationships between repeats at each level and facilitates visualization of the results.

Availability: http://bioserv.rpbs.jussieu.fr/swelfe

Contact: annela{at}abi.snv.jussieu.fr

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Burkhard Rost

Received on February 7, 2008; revised on May 13, 2008; accepted on May 14, 2008

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