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Background: Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II transposable elements present in a high number of conserved copies in eukaryote genomes. An accurate identification of these elements can help to shed light on the mechanisms controlling genome evolution and gene regulation. The structure and distribution of these elements are well-defined and therefore computational approaches can be used to identify [ver mas...]
dc.contributor.authorCrescente, Juan Manuel
dc.contributor.authorZavallo, Diego
dc.contributor.authorHelguera, Marcelo
dc.contributor.authorVanzetti, Leonardo Sebastian
dc.date.accessioned2018-10-17T12:33:16Z
dc.date.available2018-10-17T12:33:16Z
dc.date.issued2018
dc.identifier.issn1471-2105
dc.identifier.otherhttps://doi.org/10.1186/s12859-018-2376-y
dc.identifier.urihttp://hdl.handle.net/20.500.12123/3607
dc.identifier.urihttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2376-y
dc.description.abstractBackground: Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II transposable elements present in a high number of conserved copies in eukaryote genomes. An accurate identification of these elements can help to shed light on the mechanisms controlling genome evolution and gene regulation. The structure and distribution of these elements are well-defined and therefore computational approaches can be used to identify MITEs sequences. Results: Here we describe MITE Tracker, a novel, open source software program that finds and classifies MITEs using an efficient alignment strategy to retrieve nearby inverted-repeat sequences from large genomes. This program groups them into high sequence homology families using a fast clustering algorithm and finally filters only those elements that were likely transposed from different genomic locations because of their low scoring flanking sequence alignment. Conclusions: Many programs have been proposed to find MITEs hidden in genomes. However, none of them are able to process large-scale genomes such as that of bread wheat. Furthermore, in many cases the existing methods perform high false-positive rates (or miss rates). The rice genome was used as reference to compare MITE Tracker against known tools. Our method turned out to be the most reliable in our tests. Indeed, it revealed more known elements, presented the lowest false-positive number and was the only program able to run with the bread wheat genome as input. In wheat, MITE Tracker discovered 6013 MITE families and allowed the first structural exploration of MITEs in the complete bread wheat genome.eng
dc.formatapplication/pdfeng
dc.language.isoeng
dc.publisherBioMed Centraleng
dc.rightsinfo:eu-repo/semantics/openAccesseng
dc.sourceBMC bioinformatics 19 : 348. (2018)eng
dc.subjectArrozes_AR
dc.subjectRiceeng
dc.subjectTrigoes_AR
dc.subjectWheateng
dc.subjectTriticum Aestivumes_AR
dc.subjectOryza Sativaes_AR
dc.subjectGenomases_AR
dc.subjectGenomeseng
dc.subjectTransposonseng
dc.subjectTransposoneses_AR
dc.subject.otherTransposable Elementeng
dc.subject.otherMITEeng
dc.subject.otherMiniature Inverted-repeat Transposable Elementseng
dc.titleMITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomeseng
dc.typeinfo:ar-repo/semantics/artículoes_AR
dc.typeinfo:eu-repo/semantics/articleeng
dc.typeinfo:eu-repo/semantics/publishedVersioneng
dc.description.origenEEA Marcos Juárezes_AR
dc.description.filFil: Crescente, Juan Manuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.description.filFil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentinaes_AR
dc.description.filFil: Helguera, Marcelo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentinaes_AR
dc.description.filFil: Vanzetti, Leonardo Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.subtypecientifico


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