Prediction of miRNA binding sites (workflow)

Workflow title

Prediction of miRNA binding sites

Provider

geneXplain GmbH

Workflow overview

Description

This workflow can help to predict miRNA binding sites. Any gene table can be used as an input gene table. At the first step the gene table is converted to Ensemble transcripts (3’ UTR’s) , which is later converted to a track. This Ensemble track is used to map against a miRmap library which derived from the mirBase database (release 20; http://www.mirbase.org).

Six different miRBase collections from release 20 are available for Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Danio rerio and Caenorhabditis elegans. Depending on the Input gene set the corresponding library can be used.

The last step of the workflow is based on the miRmap method (analyses/Galaxy/microRNA/mirmap; http://mirmap.ezlab.org), published by Vejnar & Zdobnov, Nucleic Acids Res. 40:11673-11683, 2012.

The result folder contains the following tables: Ensembl transcript, Site output with all predicted miRNA binding sites, Site output track for visualization of predicted miRNA sites, Summary output and Transcript region track.

 

Parameters

Input gene table

Species

Transcript region

mirBase collection

Result folder