Application of the Ramanujan Fourier Transform for the analysis of secondary structure content in amino acid sequences.
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.
Mainardi
L T
LT
Department of Biomedical Engineering, Polytechnic University of Milan, 20133 Milano, Italy. luca.mainardi@biomed.polimi.it
Pattini
L
L
Cerutti
S
S
D000596:Amino Acids; D016208:Databases, Factual; D005583:Fourier Analysis; D006801:Humans; D008961:Models, Structural; D008962:Models, Theoretical; D017433:Protein Structure, Secondary; D020539:Sequence Analysis, Protein; D012815:Signal Processing, Computer-Assisted
D000596:Amino Acids