{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,4,28]],"date-time":"2023-04-28T00:41:09Z","timestamp":1682642469353},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Palindromic sequences, or inverted repeats (IRs), in DNA sequences involve important biological processes such as DNA\u2013protein 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.<\/jats:p>\n               <jats:p>Availability and implementation: The source code is freely available on (http:\/\/bioinfolab.miamioh.edu\/bioinfolab\/palindrome.php)<\/jats:p>\n               <jats:p>Contact: \u00a0liangc@miamioh.edu or karroje@miamioh.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt651","type":"journal-article","created":{"date-parts":[[2013,11,10]],"date-time":"2013-11-10T01:09:20Z","timestamp":1384045760000},"page":"887-888","source":"Crossref","is-referenced-by-count":13,"title":["A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences"],"prefix":"10.1093","volume":"30","author":[{"given":"Sutharzan","family":"Sreeskandarajan","sequence":"first","affiliation":[{"name":"1 Department of Biology, 2Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and 3State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michelle M.","family":"Flowers","sequence":"additional","affiliation":[{"name":"1 Department of Biology, 2Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and 3State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John E.","family":"Karro","sequence":"additional","affiliation":[{"name":"1 Department of Biology, 2Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and 3State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chun","family":"Liang","sequence":"additional","affiliation":[{"name":"1 Department of Biology, 2Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and 3State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China"},{"name":"1 Department of Biology, 2Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and 3State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China"},{"name":"1 Department of Biology, 2Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and 3State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,11,8]]},"reference":[{"key":"2023012710445376000_btt651-B1","doi-asserted-by":"crossref","first-page":"2632","DOI":"10.1073\/pnas.79.8.2632","article-title":"Inverted repeats of Tn5 are transposable elements","volume":"79","author":"Berg","year":"1982","journal-title":"Proc. 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