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PMID: 15980460 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

REPPER--repeats and their periodicities in fibrous proteins.

Nucleic acids research ·Vol. 33 ·No. Web Server issue ·2005-07-01 ·Pages W239-43

Gruber M, Söding J, Lupas AN

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.

MeSH Terms
Adhesins, Bacterial/chemistry Internet Protein Structure, Secondary Proteins/chemistry Repetitive Sequences, Amino Acid Sequence Alignment Sequence Analysis, Protein/methods Software
Chemicals
Adhesins, Bacterial Proteins YadA protein, Yersinia
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Gruber Markus
Max-Planck Institute for Developmental Biology Spemannstr. 35, 72076 Tübingen, Germany. markus.gruber@tuebingen.mpg.de
Söding Johannes
Lupas Andrei N
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gki405
Email
markus.gruber@tuebingen.mpg.de
Published
2005-07-01
Pages
W239-43
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1160166
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gki405 PMC Full Text View journal details
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