Small RNA Tools

Over the years, we have developed a number of tools for plant-centric small RNA analyses. These tools facilitate our work and are key components used in many of our publications. Some are described in publications focused on the tool, and others are unpublished; some are available with a web interface, and some as stand-alone, command-line tools. We hope that you will also find them useful.

Some of the tool links below may not work as we are currently in the process of transferring all our web resources from the Danforth Center to the UC Davis.

miRNA Similarity

miRNA Similarity Analysis

This web tool is useful for comparisons of small RNA sequences to rapidly find near matches or homologs of microRNAs and other plant small RNAs.

miTRATA

miRNA Truncation & Tailing Analysis

The first web-based tool for the analysis of 3’ modifications of microRNAs including the loss or gain of nucleotides relative to the canonical sequence. See Patel et al. (2015) Bioinformatics.

VARNISH

Vetting & Analysis of RNA for In Situ Hybridization

An online software tool for designing probes used for super resolution imaging of RNAs with Points Accumulation for Imaging in Nanoscale Topography (RNA-PAINT). See Huang et al. (2020) Nucleic Acids Research.

sPARTA

Small RNA-PARE Targets Analyzer

A high performance software for the validation of plant miRNA or sRNA targets with PARE data. See Kakrana et al. (2014) Nucleic Acids Research.

Target Prediction

miRNA Target Prediction

A prediction web tool identifying potential targets of microRNAs or other small RNAs in the genome or set of sequences chosen or submitted.

Reverse Target Prediction

miRNA Reverse Target Prediction

This tool is useful when no genome is available or when the user wants to assess a specific genomic sequence for targets of small RNAs.

comPARE

PARE Validated miRNA Targets

A web resource for exploring miRNA-target interactions validated by PARE data. See Kakrana et al. (2014) Nucleic Acids Research.