AmiRNA Designer

A tool dedicated for the design of artificial microRNAs

Introduction

AmiRNA Designer is a tool dedicated to design artificial micro RNAs (amiRNA and amiRNA* sequences) on the basis on the sequential data provided by the user.

Using AmiRNA Designer

Download the latest version of AmiRNA Designer.
Unpack the the archive content and run setup.exe. The AmiRNA Designer will install automatically.

Download the latest version of the manual for AmiRNA Designer.

Exemplary input files

AmiRNA Designer is equipped with the user friendly interface. The expected input is a target gene sequence, which can be loaded as a fasta file or a plain text in a copy-paste mode. Datasets necessary for thermodynamic profiles generation are loaded as parsed text files from selected databases.

Description of the AmiRNA Designer input files can be found here.

Download the exemplary input datasets for AmiRNA Designer.

Off-target effect

The results obtained by AmiRNA Designer can be analysed for the off-target effect, using Perl scripts written for this purpose. The method to determine the direct interaction between the mRNA and amiRNA or the mRNA and amiRNA* is based on the Perl regular expressions. For each miRNA and miRNA*, the search for the binding site is performed along the entire transcripts with the shift of one nucleotide.

Download the exemplary input, output datasets and Perl scripts to conduct the off-target analysis of the results obtained from AmiRNA Designer.