Frontiers in Plant Science (Aug 2019)

siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction

  • Stefanie Lück,
  • Tino Kreszies,
  • Marc Strickert,
  • Patrick Schweizer,
  • Markus Kuhlmann,
  • Dimitar Douchkov

DOI
https://doi.org/10.3389/fpls.2019.01023
Journal volume & issue
Vol. 10

Abstract

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RNA interference (RNAi) is a technique used for transgene-mediated gene silencing based on the mechanism of posttranscriptional gene silencing (PTGS). PTGS is an ubiquitous basic biological phenomenon involved in the regulation of transcript abundance and plants’ immune response to viruses. PTGS also mediates genomic stability by silencing of retroelements. RNAi has become an important research tool for studying gene function by strong and selective suppression of target genes. Here, we present si-Fi, a software tool for design optimization of RNAi constructs necessary for specific target gene knock-down. It offers efficiency prediction of RNAi sequences and off-target search, required for the practical application of RNAi. si-Fi is an open-source (CC BY-SA license) desktop software that works in Microsoft Windows environment and can use custom sequence databases in standard FASTA format.

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