psRNATarget: A Plant Small RNA Target Analysis Server (2017 Update)

Plant regulatory small RNAs (sRNA), including most of microRNAs (miRNAs) and a subset of small interfering RNAs (phasiRNAs), play important roles in gene expression regulation. Although being generated from genetically distinct biogenesis pathways, the regulatory sRNAs ranging from 20-22 nucleotides in length share the same mechanism that guides posttranscriptional gene silencing through mRNA degradation or translational inhibition.

The psRNATarget was specifically developed to identify target transcripts of these sRNAs through i) analyzing complementary matching between sRNA and target using a proven pre-defined scoring schema; and ii) evaluating target site accessibility by calculating unpaired energy (UPE). The 2017 update introduces significantly improved analytical capabilities and capacities: 1) we have implemented a new complementary matching scoring module. Users now can customize the complementary scoring schemas to analyze target genes of regulatory sRNAs, including the non-canonical targets with long bulge on target sequences. 2) The new psRNATarget is capable of transmitting and analyzing ‘big’ data from next generation sequencing platforms through the following implementation: i) optimizing pre-check module of pipeline to remove redundant sequences; ii) enabling resumable and chunked uploading using HTML5 API; and iii) allocating significantly more computing nodes to psRNATarget’s backend Linux cluster.