Application of the Ramanujan Fourier Transform for the Analysis of Secondary Structure Content in Amino Acid Sequences

L. T. Mainardi; L. Pattini; S. Cerutti

doi:10.1055/s-0038-1625380

Methods of Information in Medicine, Table of Contents

Methods Inf Med 2007; 46(02): 126-129
DOI: 10.1055/s-0038-1625380

Original Article

Schattauer GmbH

Application of the Ramanujan Fourier Transform for the Analysis of Secondary Structure Content in Amino Acid Sequences

L. T. Mainardi

¹Department of Biomedical Engineering, Polytechnic University of Milan, Milan, Italy

,

L. Pattini

¹Department of Biomedical Engineering, Polytechnic University of Milan, Milan, Italy

,

S. Cerutti

¹Department of Biomedical Engineering, Polytechnic University of Milan, Milan, Italy

› Author Affiliations

Abstract

Summary

Objective : A novel method is presented for the investigation of protein properties of sequences using Ramanujan Fourier Transform (RFT).

Methods : The new methodology involves the preprocessing of protein sequence data by numerically encoding it and then applying the RFT. The RFT is based on projecting the obtained numerical series on a set of basis functions constituted by Ramanujan sums (RS). In RS components, periodicities of finite integer length, rather than frequency, (as in classical harmonic analysis) are considered.

Results : The potential of the new approach is documented by a few examples in the analysis of hydrophobic profiles of proteins in two classes including abundance of alpha-helices (group A) or beta-strands (group B). Different patterns are provided as evidence.

Conclusions : RFT can be used to characterize the structural properties of proteins and integrate complementary information provided by other signal processing transforms.

Keywords

Frequency analysis - secondary structures - signal processing - Ramanujan series

Full Text

References

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