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. 2011 Jul;39(Web Server issue):W155-9.
doi: 10.1093/nar/gkr319. Epub 2011 May 27.

psRNATarget: a plant small RNA target analysis server

Xinbin Dai  1 , Patrick Xuechun Zhao
Affiliations

psRNATarget: a plant small RNA target analysis server

Xinbin Dai et al. Nucleic Acids Res. 2011 Jul.

Abstract

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/.

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Figures

Figure 1.
Figure 1.
A set of parameters for adjusting the behavior of back-end pipeline of psRNATarget server.
Figure 2.
Figure 2.
A list of comprehensive miRNA/target site pairs along with query and sort tools on top of each output page.
See this image and copyright information in PMC

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