Please copy and paste your miRNA sequences here:

Now choose a transcript library:

And set the parameters:

Penalty score should be lower than (lower is better):(0.0-7.0)
Supposed cleavage site after position:(2-30)
Number of bulges at the cleavage site (in the range of 2 nt up/downstream flanking):(1-5)
Maximal allowed mismatches and G:U pairs (suggest to set as penalty+1):(0-7)
Maximal allowed mismatches (suggest to set as penalty-1):(0-7)
Maximal allowed mismatches in seed region (here define seed region as the 2nd to 8th nt in small RNA):(0-7)

About the Server

MiRNA target mimics, or miRNA target decoys, are endogenous RNAs that can negatively regulate the miRNA activities. The target mimics always contain a motif with sequence complematarity to the miRNA, but the pairing is interrupted by a bulge around the supposed cleavage site (often at 10-11 nt on miRNA). Because of the bulge, miRNA target mimics are not cleaved, instead, they sequesters the miRNA and reduces its active level.

MiRNA target mimics are proved to be powerful tools to analyze functions of miRNA families. Meanwhile, precise manipulation of plant endogenous RNA regulatory networks by engineering miRNA target mimics are expected to enhance plant development and their ability to respond to environmental stresses.

Our software is developed to predict plant miRNA endougenous target mimics in genome-wide scale. We provide pre-loaded transcript sequences of coding and non-coding regions from 4 species as a candidate pool of target mimics and as many as 6 tunable parameters.

For detailed explanation of the usages of the server, please check the manual.

Download

Image 4

Download and install psMimic source code:

PsMimic local version is provided in need of high throughput local plant small RNA target mimicry prediction. The local version is written in C with a Perl wrapper. In order to install and use the local version of psMimic, you need to have a Unix/Linux system, a C compiler and a Perl interpreter.

Version   Source   Date
psMimic v1.1psMimic_v1.1.tar.gz04-13-2016

To install psMimic:
tar zxvf psMimic_v1.1.tar.gz
cd psMimic_v1.1
./configure -p <INSTALLATION_PATH>
make
make install

Run psMimic:

psRobot_mim -s <SMALL_RNA> -t <TARGET_MIMICRY> -o <OUTPUT_FILE>

For detailed usage and alternative parameter settings, please run:

psRobot_mim -h

Manual