Computational tools for plant small RNA detection and categorization

Lionel Morgado, Frank Johannes
2017 Briefings in Bioinformatics  
Small RNAs (sRNAs) are important short-length molecules with regulatory functions essential for plant development and plasticity. High-throughput sequencing of total sRNA populations has revealed that the largest share of sRNA remains uncategorized. To better understand the role of sRNA-mediated cellular regulation, it is necessary to create accurate and comprehensive catalogues of sRNA and their sequence features, a task that currently relies on nontrivial bioinformatic approaches. Although a
more » ... arge number of computational tools have been developed to predict features of sRNA sequences, these tools are mostly dedicated to microRNAs and none integrates the functionalities necessary to describe units from all sRNA pathways thus far discovered in plants. Here, we review the different classes of sRNA found in plants and describe available bioinformatics tools that can help in their detection and categorization. Lionel Morgado is a PhD candidate at the Groningen Bioinformatics Centre (University of Groningen, The Netherlands). The focus of his research is the development of high-throughput computational methods to study small RNAs in plants. Frank Johannes is an assistant professor for population epigenetics and epigenomics at the Technical University of Munich. He combines bioinformatic and statistical genetic approaches with high-throughput molecular data to characterize patterns of epigenetic variation in populations of plants. The goal is to understand how this variation arises, how stable it is across generations and to what extent it determines agriculturally and evolutionarily relevant plant traits. www.johanneslab.org.
doi:10.1093/bib/bbx136 pmid:29059285 fatcat:2cgfz3s4tfdx5oo2vwahhq2l3e