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


METHODS
The source code is freely available on (http://bioinfolab.miamioh.edu/bioinfolab/palindrome.php)


BACKGROUND
liangc@miamioh.edu or karroje@miamioh.edu


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Biology, Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
Sutharzan
S
Sreeskandarajan
Michelle M
MM
Flowers
John E
JE
Karro
Chun
C
Liang
D000465:Algorithms; D016678:Genome; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software