About Our miRNA Tools

Our lab has developed a number of tools for the analysis of plant microRNAs or other types of small RNAs. These tools are available from our website, using either the tabs above or the links in the descriptions below.


The comPARE web resource for exploring miRNA-target interactions validated by PARE data. It is a resource to sort and examine PARE-validated miRNA::target interactions. Potential applications include verification of miRNAs and their targets, comparison of targets of miRNAs across single or multiple species; and the mining of validated interactions at a genome scale. The miRNAs are taken "as is" from miRBase and it is well-known that there are many incorrectly annotated miRNAs in miRBase (i.e. siRNAs or unvalidated predictions). The validation data are based on PARE analysis (described in this paper). See our paper discussing this tool.


Download sPARTA (small RNA-PARE Targets Analyzer), a high performance software for the validation of plant miRNA or sRNA targets with PARE (Parallel Analysis of Read Ends) data. It is optimized for whole genome analyses. sPARTA includes a built-in, plant-focused target prediction module (aka 'miRferno'); miRferno can be run independently of sPARTA as a stand-alone program. sPARTA is quite fast: for example, it can predict and validate targets for 337 Arabidopsis miRNAs (miRBASE v. 20) against the whole genome in 2.5 minutes. sPARTA is designed to run on servers/nodes for whole-genome analysis but it is highly scalable and memory efficient, thus can be used on (quad-core or above) desktops as well. See our paper discussing this tool.


Web version of sPARTA, small RNA-PARE target analyzer, for identification and PARE-based validation of plant miRNAs.


miTRATA (microRNA-Truncation and Tailing Analysis) is 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. miTRATA is implemented in Python (version 3) and employs parallel processing modules to enhance its scalability when analyzing multiple small RNA (sRNA) sequencing datasets. It utilizes miRBase, currently version 21, as a source of known microRNAs for analysis. miTRATA notifies user(s) via email to download as well as visualize the results online. miTRATA’s strengths lies in 1) its biologist-focused web interface, 2) improved scalability via parallel processing, and 3) its uniqueness as a first web-tool to perform microRNA truncation and tailing analysis.