title: Application of intelligent techniques for classification of bacteria using protein sequence-derived features.
abstract: Standard molecular experimental methodologies and mathematical procedures often fail to answer many phylogeny and classification related issues. Modern artificial intelligent-based techniques, such as radial basis function, genetic algorithm, artificial neural network, and support vector machines are of ample potential in this regard. Reliance on a large number of essential parameters will aid in enhanced robustness, reliability, and better accuracy as opposed to single molecular parameter. This study was conducted with dataset of computed protein physicochemical properties belonging to 20 different bacterial genera. A total of 57 sequential and structural parameters derived from protein sequences were considered for the initial classification. Feature selection based techniques were employed to find out the most important features influencing the dataset. Various amino acids, hydrophobicity, relative sulfur percentage, and codon number were selected as important parameters during the study. Comparative analyses were performed applying RapidMiner data mining platform. Support vector machine proved to be the best method with maximum accuracy of more than 91%.
authors: Bioinformatics Group, Biology Division, Indian Institute of Chemical Technology (CSIR), Tarnaka, Uppal Road, Hyderabad, AP, India.
authors: Amit Kumar
authors: AK
authors: Banerjee
authors: Vadlamani
authors: V
authors: Ravi
authors: U S N
authors: US
authors: Murty
authors: Neelava
authors: N
authors: Sengupta
authors: Batepatti
authors: B
authors: Karuna
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001185:Artificial Intelligence; D001419:Bacteria / Q000145:classification* / Q000201:enzymology*; D015373:Bacterial Typing Techniques / Q000379:methods*; D000071677:Histidine Kinase; D008969:Molecular Sequence Data; D011494:Protein Kinases / Q000737:chemistry* / Q000378:metabolism*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011494:Protein Kinases; D000071677:Histidine Kinase