A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences.

ABSTRACT:

Summary

Palindromic sequences, or inverted repeats (IRs), in DNA sequences involve important biological processes such as DNA-protein binding, DNA replication and DNA transposition. Development of bioinformatics tools that are capable of accurately detecting perfect IRs can enable genome-wide studies of IR patterns in both prokaryotes and eukaryotes. Different from conventional string-comparison approaches, we propose a novel algorithm that uses a cumulative score system based on a prime number representation of nucleotide bases. We then implemented this algorithm as a MATLAB-based program for perfect IR detection. In comparison with other existing tools, our program demonstrates a high accuracy in detecting nested and overlapping IRs.

Availability and implementation

The sou

SUBMITTER: Sreeskandarajan S 

PROVIDER: S-EPMC3957078 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature