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. 2018 Jul 2;46(W1):W49-W54.
doi: 10.1093/nar/gky316.

psRNATarget: a plant small RNA target analysis server (2017 release)

Xinbin Dai  1 , Zhaohong Zhuang  1 , Patrick Xuechun Zhao  1
Affiliations

psRNATarget: a plant small RNA target analysis server (2017 release)

Xinbin Dai et al. Nucleic Acids Res. .

Abstract

Plant regulatory small RNAs (sRNAs), which include most microRNAs (miRNAs) and a subset of small interfering RNAs (siRNAs), such as the phased siRNAs (phasiRNAs), play important roles in regulating gene expression. Although generated from genetically distinct biogenesis pathways, these regulatory sRNAs share the same mechanisms for post-translational gene silencing and translational inhibition. psRNATarget was developed to identify plant sRNA targets by (i) analyzing complementary matching between the sRNA sequence and target mRNA sequence using a predefined scoring schema and (ii) by evaluating target site accessibility. This update enhances its analytical performance by developing a new scoring schema that is capable of discovering miRNA-mRNA interactions at higher 'recall rates' without significantly increasing total prediction output. The scoring procedure is customizable for the users to search both canonical and non-canonical targets. This update also enables transmitting and analyzing 'big' data empowered by (a) the implementation of multi-threading chunked file uploading, which can be paused and resumed, using HTML5 APIs and (b) the allocation of significantly more computing nodes to its back-end Linux cluster. The updated psRNATarget server has clear, compelling and user-friendly interfaces that enhance user experiences and present data clearly and concisely. The psRNATarget is freely available at http://plantgrn.noble.org/psRNATarget/.

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Figures

Figure 1.
Figure 1.
A screenshot showing the three functional tabs of the psRNATarget, allowing users to (i) upload and search miRNAs against the pre-loaded target transcript libraries, (ii) upload and search target candidates against published miRNA sequences downloaded from miRBase or (iii) upload both miRNA and target sequences and search for potential miRNA-target pairs.
Figure 2.
Figure 2.
A screenshot of the psRNATarget web interface for choosing complementary matching scoring schema and customizing both required and optional parameters. A context help prompt will appear when the user leaves the mouse cursor on the text labels of any input field for more than one second.
Figure 3.
Figure 3.
A screenshot of the psRNATarget output page. Users can use the integrated search and sort functions to further filter the predicted miRNA–mRNA interactions.
See this image and copyright information in PMC

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