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

TLDR

Plant regulatory small RNAs, including miRNAs and phasiRNAs, modulate gene expression through post‑translational silencing and translational inhibition. The server was created to predict plant sRNA targets by scoring sequence complementarity and target site accessibility, and the 2017 update introduces a new scoring scheme that improves recall without inflating predictions. The updated tool offers customizable scoring for canonical and non‑canonical targets, supports large datasets via multi‑threaded chunked uploads and expanded backend nodes, and provides a clear, user‑friendly interface. The updated psRNATarget server is freely accessible at http://plantgrn.noble.org/psRNATarget/.

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/.