Mohammed Abo-Zahhad Abo-Zeid; Sabah M. Ahmed; Shimaa A. Abd-Elrahman

Genomic Analysis and Classification of Exon and Intron Sequences Using DNA Numerical Mapping Techniques

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Author(s)

Mohammed Abo-Zahhad Abo-Zeid ^1,* Sabah M. Ahmed ¹ Shimaa A. Abd-Elrahman ¹

1. Electrical and Electronics Engineering Department, Faculty of Engineering, Assiut University, Assiut, Egypt

* Corresponding author.

DOI: https://doi.org/10.5815/ijitcs.2012.08.03

Received: 22 Sep. 2011 / Revised: 14 Jan. 2012 / Accepted: 12 Mar. 2012 / Published: 8 Jul. 2012

Index Terms

Genomic Signal Processing, DNA and Proteins Sequences, Numerical Mapping, Codon, Exons and Introns, Short Time Fourier Transform

Abstract

Using digital signal processing in genomic field is a key of solving most problems in this area such as prediction of gene locations in a genomic sequence and identifying the defect regions in DNA sequence. It is found that, using DSP is possible only if the symbol sequences are mapped into numbers. In literature many techniques have been developed for numerical representation of DNA sequences. They can be classified into two types, Fixed Mapping (FM) and Physico Chemical Property Based Mapping (PCPBM (. The open question is that, which one of these numerical representation techniques is to be used? The answer to this question needs understanding these numerical representations considering the fact that each mapping depends on a particular application. This paper explains this answer and introduces comparison between these techniques in terms of their precision in exon and intron classification. Simulations are carried out using short sequences of the human genome (GRch37/hg19). The final results indicate that the classification performance is a function of the numerical representation method.

Cite This Paper

Mohammed Abo-Zahhad, Sabah M. Ahmed, Shimaa A. Abd-Elrahman, "Genomic Analysis and Classification of Exon and Intron Sequences Using DNA Numerical Mapping Techniques", International Journal of Information Technology and Computer Science(IJITCS), vol.4, no.8, pp.22-36, 2012. DOI:10.5815/ijitcs.2012.08.03

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International Journal of Information Technology and Computer Science (IJITCS)