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

Author(s): Achuthsankar S. Nair | Sivarama Pillai Sreenadhan

Journal: Bioinformation
ISSN 0973-2063

Volume: 1;
Issue: 6;
Start page: 197;
Date: 2006;
Original page

Keywords: Fourier | locating exons | gene finding | electron-ion interaction pseudopotential (EIIP)

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.

Tango Jona
Tangokurs Rapperswil-Jona

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