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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  
dc.contributor.author
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  
dc.subject
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  
dc.description.fil
Fil: Santos, Juan C.. Saint John´s University; Estados Unidos  
dc.description.fil
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