siVirus: web-based antiviral siRNA design software for highly divergent viral sequences

Abstract

siVirus (http://siVirus.RNAi.jp/) is a web-based online software system that provides efficient short interfering RNA (siRNA) design for antiviral RNA interference (RNAi). siVirus searches for functional, off-target minimized siRNAs targeting highly conserved regions of divergent viral sequences. These siRNAs are expected to resist viral mutational escape, since their highly conserved targets likely contain structurally/functionally constrained elements. siVirus will be a useful tool for designing optimal siRNAs targeting highly divergent pathogens, including human immunodeficiency virus (HIV), hepatitis C virus (HCV), influenza virus and SARS coronavirus, all of which pose enormous threats to global human health.

Figure 1

(A) The degree of conservation is calculated for all possible siRNA candidates (total 4 417 157) targeting every other position of 495 HIV-1 sequences. (B) The efficacy predictions of these 4 417 157 siRNA candidates based on three different guidelines: Ui-Tei et al. (6), Reynolds et al. (7) and Amarzguioui et al. (8). (C) Typical output of siVirus for designing anti-HIV siRNAs. Sequence information, efficacy predictions, off-target search results and the degrees of conservation are shown.