Plant & Animal Genomes XIII Conference Plant & Animal Genomes XIII ConferenceJanuary 15-19, 2005
Town & Country Convention Center
San Diego, CA
As an essential mechanism in multicellular eukaryotes to regulate gene expression, RNA interference (RNAi) provides a revolutionary approach for gene function analysis and a promising strategy for therapeutics. Small interfering RNAs (siRNAs) are involved in the RNAi pathway as sequence-specific guides to post-transcriptionally suppress or inactivate the complementary target mRNAs. It is fundamental to avoid any un-intended genes to be silenced by the siRNA in gene function studies. Since these small RNAs recognize their targets by base pairing, potential off-targets can be predicted by computational sequence similarity search approaches. However, currently published online tools simply use BLAST to predict siRNA off-targets. As a heuristic algorithm, BLAST may miss many off-targets with mismatches tolerable in siRNA-target recognition. Therefore, a web-based tool ‘RNAi Target Screener’, available at http://bioinfo3.noble.org/targetscreener.htm, has been developed. The tool implements an algorithm which guarantees finding all potential target genes or sites in the target gene. Since plant microRNAs (miRNAs) also recognize their targets simply by sequence complementarity, the tool can also be used to predict plant miRNA targets. The user can submit a siRNA or miRNA as the query, specify the maximum mismatches, and choose a target dataset from a collection of genome mRNAs or non-redundant gene transcripts for plant and animal species. The predicted targets are output in the order of mismatches, which are highlighted in colors. Verified using randomly generated small RNAs as well as published siRNAs and plant miRNAs, the tool should be particularly useful in siRNA-induced gene silencing to predict off-target genes.