Identifying inverted repeat structure in DNA sequences using correlation framework

The detection of inverted repeat structure is important in biology because it has been associated with large biological function. This paper presents a framework for identifying inverted repeat structure present in DNA sequence. Based on the correlation framework, the algorithm is divided into two stages. In the first stage the position and length of contiguous inverted repeats are identified based on the input parameters using correlation function. Later on in the second stage maximal inverted repeats are constructed by merging of continuous inverted repeats. The advantage of the framework is that it can be successfully used for identifying both exact and inexact inverted repeats, returning maximal inverted repeat. Additionally, the framework does not need the user to specify parameters which require knowledge of system details. Experiments were performed on various chromosomes of Saccharomyces cerevisiae (baker's yeast) genome data available at NCBI website and some of the typical results are presented in this paper.