BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data

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dc.catalogadorgjm
dc.contributor.authorMoraga, Carol
dc.contributor.authorSanchez, Evelyn
dc.contributor.authorFerrarini, Mariana Galvão
dc.contributor.authorGutiérrez Ilabaca, Rodrigo Antonio
dc.contributor.authorVidal, Elena A.
dc.contributor.authorSagot, Marie-France
dc.date.accessioned2024-01-30T15:23:31Z
dc.date.available2024-01-30T15:23:31Z
dc.date.issued2020
dc.description.abstractMicroRNAs (miRNAs) are small non-coding RNAs that are key players in the regulation of gene expression. In the last decade, with the increasing accessibility of high-throughput sequencing technologies, different methods have been developed to identify miRNAs, most of which rely on pre-existing reference genomes. However, when a reference genome is absent or is not of high quality, such identification becomes more difficult. In this context, we developed BrumiR, an algorithm that is able to discover miRNAs directly and exclusively from sRNA-seq data. We benchmarked BrumiR with datasets encompassing animal and plant species using real and simulated sRNA-seq experiments. The results demonstrate that BrumiR reaches the highest recall for miRNA discovery, while at the same time being much faster and more efficient than the state-of-the-art tools evaluated. The latter allows BrumiR to analyze a large number of sRNA-seq experiments, from plants or animals species. Moreover, BrumiR detects additional information regarding other expressed sequences (sRNAs, isomiRs, etc.), thus maximizing the biological insight gained from sRNA-seq experiments. Finally, when a reference genome is available, BrumiR provides a new mapping tool (BrumiR2ref) that performs an a posteriori exhaustive search to identify the precursor sequences. The code of BrumiR is freely available at https://github.com/camoragaq/BrumiR.
dc.fechaingreso.objetodigital2024-06-11
dc.fuente.origenORCID
dc.identifier.doi10.1101/2020.08.07.240689
dc.identifier.urihttps://doi.org/10.1101/2020.08.07.240689
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/81074
dc.information.autorucFacultad de Ciencias Biológicas; Gutiérrez Ilabaca, Rodrigo Antonio; 0000-0002-5961-5005; 86782
dc.language.isoen
dc.nota.accesoContenido completo
dc.rightsacceso abierto
dc.subject.ddc610
dc.subject.deweyMedicina y saludes_ES
dc.titleBrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data
dc.typepreprint
sipa.codpersvinculados86782
sipa.trazabilidadORCID;2024-01-15
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