StructRNAfinder: an automated pipeline and web server for RNA families prediction

Background: The 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.Programa Becas Iberoamerica, Jovenes Profesores e Investigadores, Santander Universidades, Chile Vicerrectoria de Investigation, Universidad Mayor, Chile Fondecyt Iniciacion, Comision National de Investigacion Cientifica y Tecnologica (CONICYT), Chile 11161020 Fondo de Financiamiento de Centro de Investigacion en Areas Prioritarias (FONDAP), CONICYT 15130011 Programa Nacional de Insercion de Capital Humano Avanzado en la Academia, PAI-CONICYT, Chile PAI79170021 Programa de Bienes Publicos Estrategicos para la Competitividad, Corporacion de Fomento de la Produccion (CORFO), Chile 16BPE-62321 Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP), Brazil 12/19278-6 Subsidio Semilia de Asignacion Flexible (SSAF), CORFO 14-SSAF-27061