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Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W239-43.

REPPER--repeats and their periodicities in fibrous proteins.

Author information

1
Max-Planck Institute for Developmental Biology Spemannstr. 35, 72076 Tübingen, Germany. markus.gruber@tuebingen.mpg.de

Abstract

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.

PMID:
15980460
PMCID:
PMC1160166
DOI:
10.1093/nar/gki405
[Indexed for MEDLINE]
Free PMC Article
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