Automatic curation of large comparative animal MicroRNA datasets

Abstract Motivation MicroRNAs form an important class of RNA regulators that has been studied extensively. The miRBase and Rfam database provide rich, frequently updated information on both pre-miRNAs and their mature forms. These data sources, however, rely on individual data submission and thus ar...

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Bibliographic Details
Published in:Bioinformatics 2019-11, Vol.35 (22), p.4553-4559
Main Authors: Yazbeck, Ali M, Stadler, Peter F, Tout, Kifah, Fallmann, Jörg
Format: Article
Language:English
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Summary:Abstract Motivation MicroRNAs form an important class of RNA regulators that has been studied extensively. The miRBase and Rfam database provide rich, frequently updated information on both pre-miRNAs and their mature forms. These data sources, however, rely on individual data submission and thus are neither complete nor consistent in their coverage across different miRNA families. Quantitative studies of miRNA evolution therefore are difficult or impossible on this basis. Results We present here a workflow and a corresponding implementation, MIRfix, that automatically curates miRNA datasets by improving alignments of their precursors, the consistency of the annotation of mature miR and miR* sequence, and the phylogenetic coverage. MIRfix produces alignments that are comparable across families and sets the stage for improved homology search as well as quantitative analyses. Availability and implementation MIRfix can be downloaded from https://github.com/Bierinformatik/MIRfix. Supplementary information Supplementary data are available at Bioinformatics online.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btz271