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

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

SUBMITTER: Marsella L 

PROVIDER: S-EPMC2687986 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature