Introduction

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.

Publications

  1. miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants.
    Cite this
    Yang X, Li L, 2011-09-01 - Bioinformatics (Oxford, England)

Credits

  1. Xiaozeng Yang
    Developer

  2. Lei Li
    Investigator

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Summary
AccessionBT006733
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByLei Li