Title: New encoded single-indicator sequences based on physico-chemical parameters for efficient exon identification

Authors: J.K. Meher; P.K. Meher; G.N. Dash; M.K. Raval

Addresses: Department of Computer Science and Engineering, Vikash College of Engineering for Women, Vikash Enclave, Bargarh, Odisha, India. ' Department of Embedded Systems, Institute for Infocomm Research, 1 Fusionopolis Way 138632, Singapore. ' Department of Physics, Sambalpur University, Jyoti Vihar, Orissa 768019, India. ' Department of Chemistry, G.M. College, Sambalpur, Orissa 768018, India

Abstract: The first step in gene identification problem based on genomic signal processing is to convert character strings into numerical sequences. These numerical sequences are then analysed spectrally or using digital filtering techniques for the period-3 peaks, which are present in exons (coding areas) and absent in introns (non-coding areas). In this paper, we have shown that single-indicator sequences can be generated by encoding schemes based on physico-chemical properties. Two new methods are proposed for generating single-indicator sequences based on hydration energy and dipole moments. The proposed methods produce high peak at exon locations and effectively suppress false exons (intron regions having greater peak than exon regions) resulting in high discriminating factor, sensitivity and specificity.

Keywords: dipole moments; GC-rich; hydration energy; indicator sequences; period-3; physico-chemical properties; single-indicator sequences; exon identification; gene identification; bioinformatics.

DOI: 10.1504/IJBRA.2012.045955

International Journal of Bioinformatics Research and Applications, 2012 Vol.8 No.1/2, pp.126 - 140

Received: 20 Jul 2010
Accepted: 18 Jan 2011
Published online: 05 Dec 2014 *

Full-text access for editors Full-text access for subscribers Purchase this article Comment on this article