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Bioinformatics. 2011 Sep 15;27(18):2614-5. doi: 10.1093/bioinformatics/btr430. Epub 2011 Jul 19.

miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants.

Author information

1
Department of Biology, University of Virginia, Charlottesville, VA 22904, USA.

Abstract

MOTIVATION:

Ultra-deep sampling of small RNA libraries by next-generation sequencing has provided rich information on the microRNA (miRNA) transcriptome of various plant species. However, few computational tools have been developed to effectively deconvolute the complex information.

RESULTS:

We sought to employ the signature distribution of small RNA reads along the miRNA precursor as a model in plants to profile expression of known miRNA genes and to identify novel ones. A freely available package, miRDeep-P, was developed by modifying miRDeep, which is based on a probabilistic model of miRNA biogenesis in animals, with a plant-specific scoring system and filtering criteria. We have tested miRDeep-P on eight small RNA libraries derived from three plants. Our results demonstrate miRDeep-P as an effective and easy-to-use tool for characterizing the miRNA transcriptome in plants.

AVAILABILITY:

http://faculty.virginia.edu/lilab/miRDP/ CONTACT: ll4jn@virginia.edu

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
21775303
DOI:
10.1093/bioinformatics/btr430
[Indexed for MEDLINE]

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