siRNA Design Tools

siSearch is designed to select siRNAs based on approaches derived from data mining of our siRNA database. We also allow common methods of siRNA design to be included in the search. This includes motif rules, energy conditions and specificity searching. In most cases the default parameters will be sufficient - [Read about siSearch - An siRNA design Program]

This tool follows the siRNA design guidelines first described by Tuschl and colleagues. In general, Ambion scientists find that ~50% of siRNAs designed using this tool will reduce target gene expression by >50%. - [Read about Ambion siRNA Target Finder]

Online RNAi design tool with a flash tutorial. - [Read about IDT RNAi Tutorial and Design Tool]

siDirect highly effective, target specific siRNA online design site. - [Read about siDirect siRNA Design Tool]

This site helps you select siRNAs to knock down your gene of interest. After entering your sequence or accession/gi number, choosing pattern for your oligo nucleotides and various filter methods, you will be presented with a list of oligos matching your criteria. From this list, select those oligos you would like to consider further. All the selected oligos will be BLASTed against RefSeq, UniGene, or Ensembl database. - [Read about siRNA at Whitehead]

This is a software tool to identify unique candidate siRNA target sequence in your cDNA sequence. - [Read about siRNA Target Finder]

siRNA Design Tool with guidelines. - [Read about RNAi Explorer from Genelink]

SDS (siRNA Design Software) is a software tool that helps to design siRNAs for silencing gene expression. The tool takes an mRNA sequence and makes use of existing design tools to output a set of candidates. These candidates are then filtered based on the secondary structure. - [Read about siRNA Design Software SDS]

Site which provides tools for siRNA by combining secondary structure with design rules. - [Read about Sirna iRNA Design Tool]