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dc.contributor.author
Femenias, Martin Miguel
dc.contributor.author
Santos, Juan C.
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Sites, Jack W. Jr.
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Avila, Luciano Javier
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Morando, Mariana
dc.date.available
2022-09-29T13:41:25Z
dc.date.issued
2022-07
dc.identifier.citation
Femenias, Martin Miguel; Santos, Juan C.; Sites, Jack W. Jr.; Avila, Luciano Javier; Morando, Mariana; ExplorATE: A new pipeline to explore active transposable elements from RNA-seq data; Oxford University Press; Bioinformatics (Oxford, England); 38; 13; 7-2022; 3361-3366
dc.identifier.issn
1367-4803
dc.identifier.uri
http://hdl.handle.net/11336/170981
dc.description.abstract
Motivation: Transposable elements (TEs) are ubiquitous in genomes and many remain active. TEs comprise an important fraction of the transcriptomes with potential effects on the host genome, either by generating deleterious mutations or promoting evolutionary novelties. However, their functional study is limited by the difficulty in their identification and quantification, particularly in non-model organisms. Results: We developed a new pipeline [explore active transposable elements (ExplorATE)] implemented in R and bash that allows the quantification of active TEs in both model and non-model organisms. ExplorATE creates TE-specific indexes and uses the Selective Alignment (SA) to filter out co-Transcribed transposons within genes based on alignment scores. Moreover, our software incorporates a Wicker-like criteria to refine a set of target TEs and avoid spurious mapping. Based on simulated and real data, we show that the SA strategy adopted by ExplorATE achieved better estimates of non-co-Transcribed elements than other available alignment-based or mapping-based software. ExplorATE results showed high congruence with alignment-based tools with and without a reference genome, yet ExplorATE required less execution time. Likewise, ExplorATE expands and complements most previous TE analyses by incorporating the co-Transcription and multi-mapping effects during quantification, and provides a seamless integration with other downstream tools within the R environment.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
Oxford University Press
dc.rights
info:eu-repo/semantics/restrictedAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject
RNA-SEQ
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TRANSPORTABLE ELEMENTS
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SELECTIVE ALIGNMENT
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CO-TRANSCRIPTION
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Bioquímica y Biología Molecular
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Ciencias Biológicas
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CIENCIAS NATURALES Y EXACTAS
dc.title
ExplorATE: A new pipeline to explore active transposable elements from RNA-seq data
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2022-07-04T19:18:47Z
dc.identifier.eissn
1367-4811
dc.journal.volume
38
dc.journal.number
13
dc.journal.pagination
3361-3366
dc.journal.pais
Reino Unido
dc.journal.ciudad
Oxford
dc.description.fil
Fil: Femenias, Martin Miguel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; Argentina
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Fil: Santos, Juan C.. Saint John´s University; Estados Unidos
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Fil: Sites, Jack W. Jr.. University Brigham Young; Estados Unidos
dc.description.fil
Fil: Avila, Luciano Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; Argentina
dc.description.fil
Fil: Morando, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; Argentina
dc.journal.title
Bioinformatics (Oxford, England)
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/https://doi.org/10.1093/bioinformatics/btac354
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/bioinformatics/article-abstract/38/13/3361/6591201?redirectedFrom=fulltext#no-access-message
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