Overview

Summary

E-RNAi is a web tool for the automated design and evaluation of RNAi reagents for a broad spectrum of organisms including Drosophila, C. elegans, Planaria and others. It can be used to design and evaluate long dsRNAs (including esiRNAs) and siRNAs.

Besides providing improved performance and flexibility, the updated version 3.0 of E-RNAi now offers batch queries and direct sequence selection of genomic regions from a genome browser interface.

E-RNAi can be accessed at http://www.e-rnai.org/.

E-RNAi features

• Design and evaluation of optimized long dsRNAs and siRNAs in batch (for up to 50 target sequences in one run) with:
  • prediction of the reagent's specificity
  • prediction of the reagent's efficiency
  • avoidance of low-complexity regions
  • standardized primer designs (for long dsRNAs)
  • mapping of reagents to the genome
  • visualization of designs in their genomic context using GBrowse
• Selection of desired target sequences via query of gene identifiers, FASTA sequences or from GBrowse
• Evaluation of RNAi reagents via sequence query
• Straight-forward design of independent RNAi reagents

The design method is not restricted to certain organisms. Organisms currently available are:

• D. melanogaster (FlyBase)
• A. pisum (AphidBase)
• H. sapiens (NCBI RefSeq)
• S. mediterranea (SmedGD)
• S. cerevisiae (EnsemblFungi)
• S. pombe (EnsemblFungi)
• C. elegans (WormBase)
• C. briggsae (WormBase)
• A. gambiae (VectorBase)
• A. aegypti (VectorBase)
• M. musculus (NCBI RefSeq)
• A. mellifera (BeeBase)
• T. castaneum (BeetleBase)

Further organisms with sequenced and annotated genomes (and where RNAi is used for functional studies) can be added to E-RNAi upon request. Please contact us at ernai(at)dkfz.de.

E-RNAi query options

The sections linked below describe how E-RNAi can be queried:

• ID or sequence input
• Input from GBrowse
• Evaluation of RNAi reagents

E-RNAi settings

Settings available with E-RNAi are described here.

E-RNAi results

Documentation of E-RNAi output.

Contact

• Thomas Horn or Michael Boutros

Reference

Thomas Horn and Michael Boutros (2010). E-RNAi: a web application for the multi-species design of RNAi reagents--2010 update. Nucleic Acids Research May 5, 2010. link to article