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Nucleic Acids Research 2005 33(Web Server Issue):W239-W243; doi:10.1093/nar/gki405
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

REPPER—repeats and their periodicities in fibrous proteins

Markus Gruber*, Johannes Söding and Andrei N. Lupas

Max-Planck Institute for Developmental Biology Spemannstr. 35, 72076 Tübingen, Germany

*To whom correspondence should be addressed. Tel: +49 7071 601 344; Fax: +49 7071 601 349; Email: markus.gruber{at}tuebingen.mpg.de

Received February 14, 2005. Revised March 21, 2005. Accepted March 21, 2005.

REPPER (REPeats and their PERiodicities) is an integrated server that detects and analyzes regions with short gapless repeats in protein sequences or alignments. It finds periodicities by Fourier Transform (FTwin) and internal similarity analysis (REPwin). FTwin assigns numerical values to amino acids that reflect certain properties, for instance hydrophobicity, and gives information on corresponding periodicities. REPwin uses self-alignments and displays repeats that reveal significant internal similarities. Both programs use a sliding window to ensure that different periodic regions within the same protein are detected independently. FTwin and REPwin are complemented by secondary structure prediction (PSIPRED) and coiled coil prediction (COILS), making the server a versatile analysis tool for sequences of fibrous proteins. REPPER is available at http://protevo.eb.tuebingen.mpg.de/repper.


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