Abstract—Classification of organisms into different categories using their genomic sequences has found its importance in the study of evolutionary characteristics of organisms and specific identification of previously unknown organisms in bio-diversity studies and related areas. Chaos game representation (CGR) uniquely represents DNA sequence in a visual format and reveals hidden patterns in it. Frequency CGR (FCGR) derived from CGR shows the frequency of sub-sequences present in the DNA sequence. In this paper, a novel method for classification of organisms based on a combination of FCGR and Artificial Neural network (ANN) is proposed. Eight categories, from the taxonomical distribution of Eukaryotic organisms are taken from NCBI and ANN is used for classification. Different con- figurations of ANN are tested and good accuracy is obtained. The way, the fractal nature of CGR helps in classification, is also investigated.
Index Terms—Artificial Neural Network, frequency chaos game representation, genome classification, mitochondrial genomes.
Vrinda V. Nair is with Government Engineering College, Thrissur, Kerala and research scholar at Centre for Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, INDIA. (e-mail:nairvrinda@rediffmail.com), Karthika Vijayan and Deepa P. Gopinath are with College of Engineering, Thiruvananthapuram, Kerala, INDIA (karthikavijayan@gmail.com, deepapgopinath@ gmail.com )and Achuthsankar S. Nair is the Hon. Director, Centre for Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, INDIA (sankar.achuth@gmail.com)
[PDF]
Cite: Vrinda V. Nair, Karthika Vijayan, Deepa P. Gopinath and Achuthsankar S. Nair, "ANN based Genome Classifier using Frequency Chaos Game Representation,"
International Journal of Engineering and Technology vol. 2, no. 3, pp. 308-312, 2010.
