title: sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software.
abstract: Parallel analysis of RNA ends (PARE) is a technique utilizing high-throughput sequencing to profile uncapped, mRNA cleavage or decay products on a genome-wide basis. Tools currently available to validate miRNA targets using PARE data employ only annotated genes, whereas important targets may be found in unannotated genomic regions. To handle such cases and to scale to the growing availability of PARE data and genomes, we developed a new tool, 'sPARTA' (small RNA-PARE target analyzer) that utilizes a built-in, plant-focused target prediction module (aka 'miRferno'). sPARTA not only exhibits an unprecedented gain in speed but also it shows greater predictive power by validating more targets, compared to a popular alternative. In addition, the novel 'seed-free' mode, optimized to find targets irrespective of complementarity in the seed-region, identifies novel intergenic targets. To fully capitalize on the novelty and strengths of sPARTA, we developed a web resource, 'comPARE', for plant miRNA target analysis; this facilitates the systematic identification and analysis of miRNA-target interactions across multiple species, integrated with visualization tools. This collation of high-throughput small RNA and PARE datasets from different genomes further facilitates re-evaluation of existing miRNA annotations, resulting in a 'cleaner' set of microRNAs.
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19714, USA Delaware Biotechnology Institute, University of Delaware, Newark, DE 19714, USA.
authors.forename: Atul
authors.initials: A
authors.lastname: Kakrana
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19714, USA Delaware Biotechnology Institute, University of Delaware, Newark, DE 19714, USA.
authors.forename: Reza
authors.initials: R
authors.lastname: Hammond
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19714, USA Delaware Biotechnology Institute, University of Delaware, Newark, DE 19714, USA.
authors.forename: Parth
authors.initials: P
authors.lastname: Patel
authors.affiliation: Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA.
authors.forename: Mayumi
authors.initials: M
authors.lastname: Nakano
authors.affiliation: Delaware Biotechnology Institute, University of Delaware, Newark, DE 19714, USA Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA meyers@dbi.udel.edu.
authors.forename: Blake C
authors.identifier: http://orcid.org/0000-0003-3436-6097
authors.initials: BC
authors.lastname: Meyers
mesh_terms: D000465:Algorithms; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D035683:MicroRNAs / Q000737:chemistry* / Q000378:metabolism; D059367:RNA Cleavage; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D018749:RNA, Plant / Q000737:chemistry* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D018749:RNA, Plant