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dc.contributorBMC Bioinformaticses
dc.contributor.authorArias Carrasco, Raúl [Chile. Universidad Mayor. Facultad de Ciencias. Centro de Genómica & BioInformática]
dc.contributor.authorVásquez Moran, Yessenia [Chile. Universidad Mayor. Facultad de Ciencias. Centro de Genómica & BioInformática]
dc.contributor.authorNakaya, Helder I. [Brasil. Universidad de Sao Paulo. Facultad de Ciencias Farmacéuticas]
dc.contributor.authorMaracaja Coutinho, Vinicius [Chile. Universidad Mayor. Facultad de Ciencias. Centro de Genómica & BioInformática]
dc.date.accessioned2018-05-07T21:39:08Z
dc.date.available2018-05-07T21:39:08Z
dc.date.issued2018-02-17
dc.identifier.citationArias-Carrasco, R; Vásquez-Morán, Y; Nakaya, HI; Maracaja-Coutinho, V. StructRNAfinder: an automated pipeline and web server for RNA families prediction. BMC Bioinformatics. 2018;19(1):55es
dc.identifier.issn1471-2105
dc.identifier.otherWOS:000425990400001
dc.identifier.urihttp://repositorio.umayor.cl/xmlui/handle/sibum/422
dc.description.abstractThe function of many noncoding RNAs (ncRNAs) depend upon their secondary structures. Over the last decades, several methodologies have been developed to predict such structures or to use them to functionally annotate RNAs into RNA families. However, to fully perform this analysis, researchers should utilize multiple tools, which require the constant parsing and processing of several intermediate files. This makes the large-scale prediction and annotation of RNAs a daunting task even to researchers with good computational or bioinformatics skills. Results: We present an automated pipeline named StructRNAfinder that predicts and annotates RNA families in transcript or genome sequences. This single tool not only displays the sequence/structural consensus alignments for each RNA family, according to Rfam database but also provides a taxonomic overview for each assigned functional RNA. Moreover, we implemented a user-friendly web service that allows researchers to upload their own nucleotide sequences in order to perform the whole analysis. Finally, we provided a stand-alone version of StructRNAfinder to be used in large-scale projects. The tool was developed under GNU General Public License (GPLv3) and is freely available at http//structrnafinder.integrativebioinformatics.me. Conclusions: The main advantage of StructRNAfinder relies on the large-scale processing and integrating the data obtained by each tool and database employed along the workflow, of which several files are generated and displayed in user-friendly reports, useful for downstream analyses and data exploration.es
dc.description.sponsorshipEste trabajo cuenta con el apoyo del Programa Becas Iberoamerica, Jovenes Profesores e Investigadores, Santander Universidades, Chile; Fondecyt Iniciacion, Comision National de Investigacion Cientifica y Tecnologica (CONICYT), Chile, grant 11161020; Programa Nacional de Insercion de Capital Humano Avanzado en la Academia, PAI-CONICYT, Chile, grant PAI79170021; Fondo de Financiamiento de Centro de Investigacion en Areas Prioritarias (FONDAP), CONICYT, grant 15130011; Programa de Bienes Publicos Estrategicos para la Competitividad, Corporacion de Fomento de la Produccion (CORFO), Chile, grant 16BPE-62321; Subsidio Semilia de Asignacion Flexible (SSAF), CORFO, grant 14-SSAF-27061-9; and Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP), Brazil, grant 12/19278-6. RAC received a PhD fellowship from Vicerrectoria de Investigation, Universidad Mayor, Chilees
dc.description.urihttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5816368/pdf/12859_2018_Article_2052.pdfen
dc.format.extentPDFes
dc.language.isoen_USes
dc.publisherChile. Universidad Mayores
dc.rightsAttribution-NonCommercial-NoDerivs 3.0 Chilees
dc.subjectModelos Predictivoses
dc.subjectModelos de covarianzaes
dc.subjectRNA sin codificaciónes
dc.subject.meshRibonucleasases
dc.titleStructRNAfinder: an automated pipeline and web server for RNA families predictiones
dc.title.alternativeStructRNAfinder: un ducto automatizado y servidor web para la predicción de familias de RNAes
dc.typeArtículo o Paperes
umayor.indizadorCOTes
umayor.politicas.sherpa/romeohttp://www.sherpa.ac.uk/romeo/issn/1471-2105/es/es
umayor.indexadoWeb of Sciencees
dc.identifier.doi10.1186/s12859-018-2052-2
umayor.indicadores.wos-(cuartil)Q2


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