Xiaozeng Yang1, Lei Li. 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.
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.
Authors: Theodore A Craig; Yuji Zhang; Andrew T Magis; Cory C Funk; Nathan D Price; Stephen C Ekker; Rajiv Kumar Journal: Zebrafish Date: 2014-03-20 Impact factor: 1.985