Mining Association Rules in Dengue Gene Sequence with Latent Periodicity

Marimuthu Thangam,Balamurugan Vanniappan

doi:10.1155/2015/839692

Marimuthu Thangam, Balamurugan Vanniappan

Open Access

https://doi.org/10.1155/2015/839692

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Abstract

The mining of periodic patterns in dengue database is an interesting research problem that can be used for predicting the future evolution of dengue viruses. In this paper, we propose an algorithm called Recurrence Finder (RECFIN) that uses the suffix tree for detecting the periodic patterns of dengue gene sequence. Also, the RECFIN finds the presence of palindrome which indicates the possibilities of formation of proteins. Further, this paper computes the periodicity of nucleic acid and amino acid sequences of any length. The periodicity based association rules are used to diagnose the type of dengue. The time complexity of the proposed algorithm is O(n2). We demonstrate the effectiveness of the proposed approach by comparing the experimental results performed on dengue virus serotypes dataset with NCBI-BLAST algorithm.

Highlights

Periodicity is the tendency where the sequences of events or values recur at particular intervals [1]
Nucleic acid sequence has the combination of nucleotide bases within deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)
The partial DNA sequence of DEN4 is shown in Box 1

Summary

Introduction

Periodicity is the tendency where the sequences of events or values recur at particular intervals [1]. Periodicity plays an important role in discovering interesting frequent patterns in any sequence including genomic sequence that is made of amino acids present in the human cells. Latent periodicity refers to the presence of hidden or reverse subsequence in the given sequence during the particular interval. Cells of the human body have a central core called nucleus, which is packaged in units known as chromosomes. Gene sequence contains a sequence of nucleic and amino acids. Nucleic acid consists of a chain of linked units called nucleotide. Nucleic acid sequence has the combination of nucleotide bases within deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). RNA is represented as the combination of four nucleotide bases adenine (A), cytosine (C), guanine (G), and uracil (U).

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