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Bioinformatics. 2019 Apr 16. pii: btz271. doi: 10.1093/bioinformatics/btz271. [Epub ahead of print]

Automatic Curation of Large Comparative Animal MicroRNA Data Sets.

Yazbeck AM1,2,3, Stadler PF1,4,5,6,7,8, Tout K2, Fallmann J1.

Author information

1
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Härtelstraße 16-18, Leipzig, Germany.
2
Doctoral School of Science and Technology, Center for Biotechnology Research, Lebanese University, Hadath Campus, Beirut, Lebanon.
3
Helmholtz Centre for Environmental Research - UFZ, Young Investigators Group Bioinformatics and Transcriptomics, Per-moserstraße 15, Leipzig, Germany.
4
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases,University Leipzig, Leipzig, Germany.
5
Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, Germany.
6
Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, Wien, Austria.
7
Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.
8
Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM, USA.

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: MIRfix can be downloaded from https://github.com/Bierinformatik/MIRfix.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online and at http://www.bioinf.uni-leipzig.de/publications/supplements/18-058.

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