The DEQOR webserver helps in the design and quality control of endoribonuclease-prepared small interfering RNAs (esiRNAs). By using state-of-the-art parameters, DEQOR will analyze each siRNA emanating from an input mRNA for its silencing potential. BLAST searches against selected transcriptomes will identify potentially cross-silenced genes. An interactive graphical output allows the user to select regions suitable for esiRNA design for further processing.
Reference: Henschel A., Buchholz F. and Habermann B. in NAR 32, W113-20, 2004: DEQOR, a web-based tool for the design and quality control of siRNAs



Pipeline of a DEQOR search:

  • full-length BLAST search identifies input query
  • in silico digest input in 21-mers
  • send in silico siRNAs to quality control and BLAST-search for checking efficiency and specificity
  • score each siRNA according to state-of-the-art parameters and potential off-targets
  • combine output and generate output

The top-ten siRNAs that have a score below 5, as well as all potentially cross-silenced genes are shown to the user. Based on the top-scoring scoring windows, the user can also design oligos for synthesis of siRNAs.



The heart of the DEQOR output window is the interactive graphical output.
Each bar in this graph represents one siRNA. Small green bars encode high-quality silencers, large black ones those with low efficiency. Red bars represent siRNAs with a perfect match to another gene and yellow bars those with one mismatch. The scoring parameters can furthermore be manipulated, showing the user potential changes in the graphical display (default parameters are shown). The sequence can be selected (blue bar) at this interface and copied to other applications.