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Article:An Evaluation of Feature Selection Approaches in Finding Amyloidogenic Regions in Protein Sequences

by Smitha Sunil Kumaran Nair, N. V. Subba Reddy, Hareesha K. S
International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 8 - Number 2
Year of Publication: 2010
Authors: Smitha Sunil Kumaran Nair, N. V. Subba Reddy, Hareesha K. S
10.5120/1189-1661

Smitha Sunil Kumaran Nair, N. V. Subba Reddy, Hareesha K. S . Article:An Evaluation of Feature Selection Approaches in Finding Amyloidogenic Regions in Protein Sequences. International Journal of Computer Applications. 8, 2 ( October 2010), 1-6. DOI=10.5120/1189-1661

@article{ 10.5120/1189-1661,
author = { Smitha Sunil Kumaran Nair, N. V. Subba Reddy, Hareesha K. S },
title = { Article:An Evaluation of Feature Selection Approaches in Finding Amyloidogenic Regions in Protein Sequences },
journal = { International Journal of Computer Applications },
issue_date = { October 2010 },
volume = { 8 },
number = { 2 },
month = { October },
year = { 2010 },
issn = { 0975-8887 },
pages = { 1-6 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume8/number2/1189-1661/ },
doi = { 10.5120/1189-1661 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T19:56:28.676450+05:30
%A Smitha Sunil Kumaran Nair
%A N. V. Subba Reddy
%A Hareesha K. S
%T Article:An Evaluation of Feature Selection Approaches in Finding Amyloidogenic Regions in Protein Sequences
%J International Journal of Computer Applications
%@ 0975-8887
%V 8
%N 2
%P 1-6
%D 2010
%I Foundation of Computer Science (FCS), NY, USA
Abstract

Amyloidogenic regions in polypeptide chains are associated with a number of diseases. Experimental evidence is compelling in favor of the hypothesis that small segments of proteins are responsible for its amyloidogenic behavior. Thus, identifying these short peptides is critical for understanding diseases associated with protein misfolding and developing sequence-targeted anti-aggregation drugs. The in silico approaches using phenomenological models based on bio-physio-chemical properties of amino acids suffer from “curse of dimensionality”. Therefore, before adopting standard classification algorithms to predict such fibril motifs, the “curse of dimensionality” needs to be solved. The present study evaluates the performance of feature selection algorithms namely filter, wrapper and embedded models in conjunction with Support Vector Machine classifier. We also propose a novel integrated feature selection strategy based on Genetic Algorithm and Support Vector Machine to get an optimal number of features in predicting the amyloid fibril-forming short stretches of peptides. In addition, we investigated the performances of feature selection models that resulted in new and complementary set of properties and concludes that the proposed integrated dimensionality reduction technique outperforms all other methods and achieves the highest sensitivity and specificity of 86% and 82% respectively.

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Index Terms

Computer Science
Information Sciences

Keywords

Amyloid fibril physicochemical properties Genetic Algorithm Support Vector Machine