General Information
| Description | A computational tool for analyzing the microRNA transcriptome in plants |
| Homepage | http://faculty.virginia.edu/lilab/miRDP/ |
Publications
miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants
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.
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