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psRNATarget: A Plant Small RNA Target Analysis Server

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: 1) reverse complementary matching between miRNA and target transcript using a proven scoring schema, and 2) target site accessibility evaluation by calculating unpaired energy (UPE) required to "open" secondary structure around miRNA’s target site on mRNA. PsRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of miRNA/target site pairs that may affect miRNA binding activity to target transcript.

PsRNATarget 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 miRNAs and transcript sequences; and outputs a comprehensive list of miRNA / target pairs along with the online tools for batch downloading, key word searching and results sorting.

» Visit psRNATarget

 

pssRNAMiner: A plant short small RNA regulatory cascade analysis server

In plants, short RNAs including ~21-nt microRNA (miRNA) and 21-nt trans-acting siRNA (ta-siRNA) compose a "miRNA -> ta-siRNA -> target gene" cascade pathway that regulates gene expression at the post-transcriptional level. In this cascade, biogenesis of ta-siRNA clusters requires 21-nt intervals (i.e. phasing) and miRNA (phase-initiator) cleavage sites on its TAS transcript. Here we report a novel web server, pssRNAMiner, which is developed to identify both the clusters of phased small RNAs as well as the potential phase-initiator.

  • To detect phased small RNA clusters, the pssRNAMiner maps input small RNAs against user-specified transcript/genomic sequences, and then identifies phased small RNA clusters by evaluating P values of hypergeometric distribution.
  • To identify potential phase-initiators, pssRNAMiner aligns input phase-initiators with transcripts of TAS candidates using the Smith-Waterman algorithm. Potential cleavage sites on TAS candidates are further identified from complementary regions by weighting the alignment expectation and its distance to detected phased small RNA clusters.

» Visit pssRNAMiner

 

PLAN: Personal bLAst Navigator

Personal-bLAst Navigator (PLAN) is a web application for organizing, managing and mining sequence alignment results based on BLAST search. Current features of PLAN include

  • Project based data organization;
  • Management of interesting queries and targets through favorites;
  • Statistical overview by query, target, gene line and plate (if applicable);
  • Alignment visualization;
  • Filtering by match score and e-value;
  • Search by accession, name and description.

PLAN also can be easily integrated into other web applications for the visualization of BLAST alignment.

» Visit PLAN Server

 

phpSSRMiner: Simple Sequence Repeat Marker Miner

phpSSRMiner effectively streamlines the process of SSR (Simple Sequence Repeat) identification, primer design, and in-silicon primer verification in a single web interface. Sequences are managed in different libraries. SSRs and primers are searchable in different manners.

» Visit phpSSRMiner Server

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