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Bioinformation. 2010 Apr 30;4(10):456-62.

Classification and clustering analysis of pyruvate dehydrogenase enzyme based on their physicochemical properties.

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1
Bioinformatics Group, Biology Division, Indian Institute of Chemical Technology, Hyderabad-500607, A.P, India.

Abstract

Biological systems are highly organized and enormously coordinated maintaining greater complexity. The increment of secondary data generation and progress of modern mining techniques provided us an opportunity to discover hidden intra and inter relations among these non linear dataset. This will help in understanding the complex biological phenomenon with greater efficiency. In this paper we report comparative classification of Pyruvate Dehydrogenase protein sequences from bacterial sources based on 28 different physicochemical parameters (such as bulkiness, hydrophobicity, total positively and negatively charged residues, α helices, β strand etc.) and 20 type amino acid compositions. Logistic, MLP (Multi Layer Perceptron), SMO (Sequential Minimal Optimization), RBFN (Radial Basis Function Network) and SL (simple logistic) methods were compared in this study. MLP was found to be the best method with maximum average accuracy of 88.20%. Same dataset was subjected for clustering using 2*2 grid of a two dimensional SOM (Self Organizing Maps). Clustering analysis revealed the proximity of the unannotated sequences with the Mycobacterium and Synechococcus genus.

KEYWORDS:

Clustering; Data Mining; KNIME; Pyruvate Dehydrogenase; Self Organizing Maps (SOM)

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