siRNAdb: a database of siRNA sequences

Abstract

Short interfering RNAs (siRNAs) are a popular method for gene-knockdown, acting by degrading the target mRNA. Before performing experiments it is invaluable to locate and evaluate previous knockdown experiments for the gene of interest. The siRNA database provides a gene-centric view of siRNA experimental data, including siRNAs of known efficacy and siRNAs predicted to be of high efficacy by a combination of methods. Linked to these sequences is information such as siRNA thermodynamic properties and the potential for sequence-specific off-target effects. The database enables the user to evaluate an siRNA's potential for inhibition and non-specific effects. The database is available at http://siRNA.cgb.ki.se.

Figure 1

Efficacy level distribution in siRNAdb.

Figure 2

View of Human AKT1 siRNA data. (a) Gene view and (b) energy profiles for a single siRNA. The first curve shows di-nucleotide binding energy values, as calculated using the method of Mathews et al. (14). The straight horizontal lines represent the binding energy at each end as calculated by Schwarz et al. (15). The second set of curves represents free energy profiles calculated using the method of Khvorova et al. (16). The black curve is that of the current siRNA. The additional green and red curves are the averaged reference values for best and worst siRNAs, respectively. All curves are calculated from antisense 5′ → 3′, which is right → left in this display.