Title

A coding measure scheme employing electron-ion interaction pseudopotential (EIIP)

Authors

Achuthsankar S. Nair¹, Sivarama Pillai Sreenadhan^2*

Affiliation

¹Hon. Director, Centre for Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India; ² Asst. Professor, Instrumentation and Control, N.S.S. College of Engineering, Palakkad-8, Kerala, India

E-mail*

srisailam@sancharnet.in; * Correspondence author

Phone

+91-491-2507108

Article Type

Hypothesis

Date

received August 15, 2006; revised September 14, 2006; accepted September 15, 2006; published online October 07, 2006

Abstract

In this paper, a revision for the existing method of locating exons by genomic signal processing technique employing four binary indicator sequences is presented. The existing method relies on the pronounced period three peaks observed in the Fourier power spectrum of the exon regions which are absent in non-coding regions. The authors have abandoned the four sequences all together and adopted a single ‘EIIP indicator sequence’ which is formed by substituting the electron-ion interaction pseudopotentials (EIIP) of the nucleotides A, G, C and T in the DNA sequence, reducing the computational overhead by 75%. The power spectrum of this sequence reveals period three peaks for exon regions. Also a number of exons have been identified which exhibit period three peaks when mapped to ‘EIIP indicator sequence’ and which do not show the same when the binary indicator sequences are employed. We could get better discrimination between exon areas and non-coding areas of a number of genomes when the sequences are mapped to EIIP indicator sequences and the power spectra of the same are taken in a sliding Kaiser window, compared to the existing method using a rectangular window which utilizes binary indicator sequences.

Keywords

Fourier; locating exons; gene finding; electron-ion interaction pseudopotential (EIIP)

Citation

Nair & Sreenadhan, Bioinformation 1(6): 197-202 (2006)

Edited by

M. K. Sakharkar

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.