An efficient algorithm to detect palindromes in DNA sequences using periodicity transform

Authors:
Ravi Gupta;Ankush Mittal;Sumit Gupta
Affiliations:
Department of Electronics and Computer Engineering, Indian Institute of Technology, Roorkee, Uttaranchal, India;Department of Electronics and Computer Engineering, Indian Institute of Technology, Roorkee, Uttaranchal, India;Department of Electronics and Computer Engineering, Indian Institute of Technology, Roorkee, Uttaranchal, India
Venue:
Signal Processing - Special section: Advances in signal processing-assisted cross-layer designs
Year:
2006

Citing 5
Cited 0

Parallel detection of all palindromes in a string

Theoretical Computer Science
Algorithms on strings, trees, and sequences: computer science and computational biology

Algorithms on strings, trees, and sequences: computer science and computational biology
STAR: an algorithm to Search for Tandem Approximate Repeats

Bioinformatics
Periodicity transforms

IEEE Transactions on Signal Processing
Detection and visualization of tandem repeats in DNA sequences

IEEE Transactions on Signal Processing

Quantified Score

Hi-index	0.00

Visualization

Abstract

This paper presents an algorithm to detect exact and inexact palindromes of a given size in DNA sequences by applying signal processing techniques. The algorithm uses modified periodicity transform to calculate compensated periodogram coefficient, which acts as a correlation parameter for detection of inexact palindromes. Detailed experiments conducted on a number of synthetic and actual DNA sequences show efficiency and accuracy of our method for detecting inexact palindromes. A comparison between our method and the standard technique shows that the increase in execution time with large sample size is significantly less in our method as compared to the standard technique.