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

文献类型： 外文期刊

第一作者： Liang, Chun

作者： Liang, Chun;Flowers, Michelle M.;Karro, John E.;Liang, Chun;Liang, Chun

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期刊名称：BIOINFORMATICS （ 影响因子：6.937； 五年影响因子：8.47 ）

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收录情况： SCI

摘要： 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.

分类号： Q81

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