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

Abstract

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.

Keywords: Covariance models; Noncoding RNAs; Pipeline; RNA family; RNA structure; Tool; Web server.

Fig. 1

a Whole pipeline implemented in StructRNAfinder. Input and output files are shown in green rhomboid; intermediate third-party or in-house scripts are shown in light blue squares; together with intermediate files generated along the process, shown in white shapes. Decisions taken along the process are shown in yellow diamonds. b General report containing the list of predicted RNA structures in E. coli strain K-12. c Detailed table for a particular predicted RNA of interest. All information related to the covariance model comparison, secondary structure inference and complete annotations are made available in this page, including a external link to Rfam database

Fig. 2

a, b Exemplary results of StructRNAfinder summary section. This section provides a general statistics of all identified RNA families in E. coli strain K-12 genome sequence. a Table showing the total numbers of each predicted RNA family according to Rfam nomenclature. b A pie-chart of the numbers shown in A. c A dynamic pie-chart with the taxonomic assignation of the 488 identified RNAs

Fig. 3

Job launcher screen showing the different parameters that a user can use when running StructRNAfinder web server