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Bioinformatics 2009 25(12):i289-i295; doi:10.1093/bioinformatics/btp232
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© 2009 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.

REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform

Luca Marsella 1,2, Francesco Sirocco 3, Antonio Trovato 2,4,5, Flavio Seno 2,4,5 and Silvio C.E. Tosatto 3,*

1CECAM, Lyon, France, 2Department of Physics, 3Department of Biology, University of Padova, Italy, 4CNISM – Unità di Padova and 5INFN - Sezione di Padova, Padova, Italy

*To whom correspondence should be addressed.


  Abstract

Motivation: Proteins with solenoid repeats evolve more quickly than non-repetitive ones and their periodicity may be rapidly hidden at sequence level, while still evident in structure. In order to identify these repeats, we propose here a novel method based on a metric characterizing amino-acid properties (polarity, secondary structure, molecular volume, codon diversity, electric charge) using five previously derived numerical functions.

Results: The five spectra of the candidate sequences coding for structural repeats, obtained by Discrete Fourier Transform (DFT), show common features allowing determination of repeat periodicity with excellent results. Moreover it is possible to introduce a phase space parameterized by two quantities related to the Fourier spectra which allow for a clear distinction between a non-homologous set of globular proteins and proteins with solenoid repeats. The DFT method is shown to be competitive with other state of the art methods in the detection of solenoid structures, while improving its performance especially in the identification of periodicities, since it is able to recognize the actual repeat length in most cases. Moreover it highlights the relevance of local structural propensities in determining solenoid repeats.

Availability: A web tool implementing the algorithm presented in the article (REPETITA) is available with additional details on the data sets at the URL: http://protein.bio.unipd.it/repetita/.

Contact: silvio.tosatto{at}unipd.it


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