detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes

Scientific Reports
Congting YeChun Liang

Abstract

Miniature inverted repeat transposable elements (MITEs) are prevalent in eukaryotic genomes, including plants and animals. Classified as a type of non-autonomous DNA transposable elements, they play important roles in genome organization and evolution. Comprehensive and accurate genome-wide detection of MITEs in various eukaryotic genomes can improve our understanding of their origins, transposition processes, regulatory mechanisms, and biological relevance with regard to gene structures, expression, and regulation. In this paper, we present a new MATLAB-based program called detectMITE that employs a novel numeric calculation algorithm to replace conventional string matching algorithms in MITE detection, adopts the Lempel-Ziv complexity algorithm to filter out MITE candidates with low complexity, and utilizes the powerful clustering program CD-HIT to cluster similar MITEs into MITE families. Using the rice genome as test data, we found that detectMITE can more accurately, comprehensively, and efficiently detect MITEs on a genome-wide scale than other popular MITE detection tools. Through comparison with the potential MITEs annotated in Repbase, the widely used eukaryotic repeat database, detectMITE has been shown to find known ...Continue Reading

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Citations

Oct 24, 2019·Ecology and Evolution·Joachim M SurmPeter J Prentis
Jun 21, 2019·Journal of Cellular Biochemistry·Vahideh AhmadzadehHabib Zarredar
Oct 5, 2018·BMC Bioinformatics·Juan Manuel CrescenteLeonardo Sebastián Vanzetti
Jul 3, 2021·Nucleic Acids Research·Xingyu LiaoJianxin Wang
Jul 22, 2021·Plant Biotechnology Journal·Michael C U Hammond-KosackKim E Hammond-Kosack

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Software Mentioned

STOWAWAY
Ubuntu
SEVERIN
MATLAB
detectMITE
Hunter
HIT
DEBOAT
CD
TOURIST6A

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