psRNATarget: a plant small RNA target analysis server

By Xinbin Dai, Patrick Xuechun Zhao. Nucleic Acids Res., 2011

1,891 citations recorded by the source corpus.

Plant endogenous non-coding short small RNAs (20–24 nt), including microRNAs (miRNAs) and a subset of small interfering RNAs (ta-siRNAs), play important role in gene expression regulatory networks (GRNs). For example, many transcription factors and development-related genes have been reported as targets of these regulatory small RNAs. Although a number of miRNA target prediction algorithms and programs have been developed, most of them were designed for animal miRNAs which are significantly different from plant miRNAs in the target recognition process. These differences demand the development of separate plant miRNA (and ta-siRNA) target analysis tool(s). We present psRNATarget, a plant small RNA target analysis server, which features two important analysis functions: (i) reverse complementary matching between small RNA and target transcript using a proven scoring schema, and (ii) target-site accessibility evaluation by calculating unpaired energy (UPE) required to ‘open’ secondary structure around small RNA’s target site on mRNA. The psRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of small RNA/target site pairs that may affect small RNA binding activity to target transcript. The psRNATarget server is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster. The server front-end integrates three simplified user-friendly interfaces to accept user-submitted or preloaded small RNAs and transcript sequences; and outputs a comprehensive list of small RNA/target pairs along with the online tools for batch downloading, key word searching and results sorting. The psRNATarget server is freely available at http://plantgrn.noble.org/psRNATarget/.

Subfields: Cancer Research, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/17ec247db8b87be2536917260e4c1dcaff8d1cc9

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Citations in the corpus

miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets (2012, background): “In addition to Homo sapiens and Mus musculus, the sequences of miRNAs and their target genes have been rapidly accumulated in other species, such as rat, fly and many plants [22,48,49].”
PsRobot: a web-based plant small RNA meta-analysis toolbox (2012, background): “Several recently developed plant miRNA target prediction tools, such as targetFinder (16,17), psRNATarget (18) and CleaveLand (19), have provided great help to researches.”
A MicroRNA Superfamily Regulates Nucleotide Binding Site–Leucine-Rich Repeats and Other mRNAs[W][OA] (2012, methodology): “…as Potential Regulators of NBS-LRR Disease Resistance Genes The psRNATarget algorithm that predicts targets of plant miRNAs (Dai and Zhao, 2011) (see Supplemental Tables 2 and 3 online) identified the mRNAs of disease resistance proteins as having binding sites for miR482…”
psRNATarget: a plant small RNA target analysis server (2017 release) (2018, methodology): “Next, the energy required to unfold secondary structure around the target site, defined as target site accessibility, is calculated using the RNAup program in the Vienna Package (16), as described in the first release of psRNATarget (12).”