ArticleNucleic acids research2014
sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Deciphering the impact of microRNAs in plant biology: a review of computational insights and experimental validation.Molecular biology reports · 2025Review
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- Detection of Ethylene Signaling Using Bioinformatics Tools in Plants.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Premeiotic 24-nt phasiRNAs are present in theProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Premeiotic 24-nt phasiRNAs are present in thebioRxiv : the preprint server for biology · 2024Article
- The importance of genotyping within the climate-smart plant breeding value chain - integrative tools for genetic enhancement programs.Frontiers in plant science · 2024Review
- Conceptual Framework of Epigenetic Analyses of Plant Responses to Sedentary Endoparasitic Nematodes.Methods in molecular biology (Clifton, N.J.) · 2024Article
- miRador: a fast and precise tool for the prediction of plant miRNAs.Plant physiology · 2023Article
- The Multiverse of Plant Small RNAs: How Can We Explore It?International journal of molecular sciences · 2022Review
- Heat-responsive microRNAs and phased small interfering RNAs in reproductive development of flax.Plant direct · 2022Article
- Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs.BMC genomics · 2022Article
- MicroRNA Databases and Tools.Methods in molecular biology (Clifton, N.J.) · 2022Article
- TarDB: an online database for plant miRNA targets and miRNA-triggered phased siRNAs.BMC genomics · 2021Article
- Reproductive phasiRNA loci and DICER-LIKE5, but not microRNA loci, diversified in monocotyledonous plants.Plant physiology · 2021Article
- MicroRNAs Regulating Autophagy in Neurodegeneration.Advances in experimental medicine and biology · 2021Article
- Reproductive phasiRNAs regulate reprogramming of gene expression and meiotic progression in rice.Nature communications · 2020Article
- Premeiotic, 24-Nucleotide Reproductive PhasiRNAs Are Abundant in Anthers of Wheat and Barley But Not Rice and Maize.Plant physiology · 2020Article
- The RNA degradome: a precious resource for deciphering RNA processing and regulation codes in plants.RNA biology · 2020Article
- PAREameters: a tool for computational inference of plant miRNA-mRNA targeting rules using small RNA and degradome sequencing data.Nucleic acids research · 2020Article
- sRNATargetDigger: A bioinformatics software for bidirectional identification of sRNA-target pairs with co-regulatory sRNAs information.PloS one · 2020Article
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5 authors.
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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.
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