MITE Tracker: An accurate approach to identify miniature inverted-repeat transposable elements in large genomes

Autores
Crescente, Juan Manuel; Zavallo, Diego; Helguera, Marcelo; Vanzetti, Leonardo Sebastián
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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 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.
Fil: Crescente, Juan Manuel. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Fisiología y Recursos Genéticos Vegetales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria. Centro Nacional de Investigaciones Agropecuarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Helguera, Marcelo. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Fisiología y Recursos Genéticos Vegetales; Argentina
Fil: Vanzetti, Leonardo Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Fisiología y Recursos Genéticos Vegetales; Argentina
Materia
MITE
RICE
TRACKER
TRANSPOSABLE ELEMENT
WHEAT
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/98361
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/98361
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling MITE Tracker: An accurate approach to identify miniature inverted-repeat transposable elements in large genomesCrescente, Juan ManuelZavallo, DiegoHelguera, MarceloVanzetti, Leonardo SebastiánMITERICETRACKERTRANSPOSABLE ELEMENTWHEAThttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Background: 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.Fil: Crescente, Juan Manuel. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Fisiología y Recursos Genéticos Vegetales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria. Centro Nacional de Investigaciones Agropecuarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Helguera, Marcelo. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Fisiología y Recursos Genéticos Vegetales; ArgentinaFil: Vanzetti, Leonardo Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Fisiología y Recursos Genéticos Vegetales; ArgentinaBioMed Central2018-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/98361Crescente, Juan Manuel; Zavallo, Diego; Helguera, Marcelo; Vanzetti, Leonardo Sebastián; MITE Tracker: An accurate approach to identify miniature inverted-repeat transposable elements in large genomes; BioMed Central; BMC Bioinformatics; 19; 1; 10-2018; 1-101471-2105CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2376-yinfo:eu-repo/semantics/altIdentifier/doi/10.1186/s12859-018-2376-yinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-10T13:00:20Zoai:ri.conicet.gov.ar:11336/98361instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-10 13:00:21.039CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv MITE Tracker: An accurate approach to identify miniature inverted-repeat transposable elements in large genomes
title MITE Tracker: An accurate approach to identify miniature inverted-repeat transposable elements in large genomes
spellingShingle MITE Tracker: An accurate approach to identify miniature inverted-repeat transposable elements in large genomes
Crescente, Juan Manuel
MITE
RICE
TRACKER
TRANSPOSABLE ELEMENT
WHEAT
title_short MITE Tracker: An accurate approach to identify miniature inverted-repeat transposable elements in large genomes
title_full MITE Tracker: An accurate approach to identify miniature inverted-repeat transposable elements in large genomes
title_fullStr MITE Tracker: An accurate approach to identify miniature inverted-repeat transposable elements in large genomes
title_full_unstemmed MITE Tracker: An accurate approach to identify miniature inverted-repeat transposable elements in large genomes
title_sort MITE Tracker: An accurate approach to identify miniature inverted-repeat transposable elements in large genomes
dc.creator.none.fl_str_mv Crescente, Juan Manuel
Zavallo, Diego
Helguera, Marcelo
Vanzetti, Leonardo Sebastián
author Crescente, Juan Manuel
author_facet Crescente, Juan Manuel
Zavallo, Diego
Helguera, Marcelo
Vanzetti, Leonardo Sebastián
author_role author
author2 Zavallo, Diego
Helguera, Marcelo
Vanzetti, Leonardo Sebastián
author2_role author
author
author
dc.subject.none.fl_str_mv MITE
RICE
TRACKER
TRANSPOSABLE ELEMENT
WHEAT
topic MITE
RICE
TRACKER
TRANSPOSABLE ELEMENT
WHEAT
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv 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 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.
Fil: Crescente, Juan Manuel. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Fisiología y Recursos Genéticos Vegetales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria. Centro Nacional de Investigaciones Agropecuarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Helguera, Marcelo. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Fisiología y Recursos Genéticos Vegetales; Argentina
Fil: Vanzetti, Leonardo Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Fisiología y Recursos Genéticos Vegetales; Argentina
description 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 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.
publishDate 2018
dc.date.none.fl_str_mv 2018-10
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/98361
Crescente, Juan Manuel; Zavallo, Diego; Helguera, Marcelo; Vanzetti, Leonardo Sebastián; MITE Tracker: An accurate approach to identify miniature inverted-repeat transposable elements in large genomes; BioMed Central; BMC Bioinformatics; 19; 1; 10-2018; 1-10
1471-2105
CONICET Digital
CONICET
url http://hdl.handle.net/11336/98361
identifier_str_mv Crescente, Juan Manuel; Zavallo, Diego; Helguera, Marcelo; Vanzetti, Leonardo Sebastián; MITE Tracker: An accurate approach to identify miniature inverted-repeat transposable elements in large genomes; BioMed Central; BMC Bioinformatics; 19; 1; 10-2018; 1-10
1471-2105
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2376-y
info:eu-repo/semantics/altIdentifier/doi/10.1186/s12859-018-2376-y
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 12.48226

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