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Bioinformatics. 2014 Jul 15;30(14):2066-7. doi: 10.1093/bioinformatics/btu147. Epub 2014 Mar 14.

comTAR: a web tool for the prediction and characterization of conserved microRNA targets in plants.

Author information

  • 1IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina.

Abstract

MOTIVATION:

MicroRNAs (miRNAs) are major regulators of gene expression in plants and animals. They recognize their target messenger RNAs (mRNAs) by sequence complementarity and guide them to cleavage or translational arrest. So far, the prediction of plant miRNA-target pairs generally relies on the use of empirical parameters deduced from known miRNA-target interactions.

RESULTS:

We developed comTAR, a web tool for the prediction of miRNA targets that is mainly based on the conservation of the potential regulation in different species. We used data generated from a pipeline applied to transcript datasets of 33 angiosperms that was used to build a database of potential miRNA targets of different plant species. The database contains information describing each miRNA-target pair, their function and evolutionary conservation, while the results are displayed in a user-friendly interface. The tool also allows the search using new miRNAs.

AVAILABILITY AND IMPLEMENTATION:

The Web site is free to all users, with no login requirements, at http://rnabiology.ibr-conicet.gov.ar/comtar.

PMID:
24632500
DOI:
10.1093/bioinformatics/btu147
[PubMed - indexed for MEDLINE]
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