Status   Guestbook   siRNA Database

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.

SDS is a web-based software with the following features:

  • It provides a unified platform for using existing software.
  • It compares the output of existing software.
  • It enhances the existing software by filtering ineffective siRNAs based on secondary structure.

Note: Version 3 of our software is released. Details of the enhancements and features of our software can be found here.

Note: Due to lack of resources, maintenance of this website will be suspended until further notice. Sorry for any inconvenience caused.

 
siRNA Design Software
mRNA Sequence Name (optional):
mRNA Sequence:
Accession Number:
Nucleotide Sequence: (All blanks and non-alphabetic characters will be removed.)
Position of start codon: (help)
Position of terminating codon: (help)
Organism:
Software: (Select one or more from the list; the default is ALL.)
Ambion (rules based on Tuschl et al.; length limit: unlimited) Timeout:
Jack (rules based on Tuschl et al.; length limit: unlimited) Timeout:
OptiRNAi (rules based on Tuschl et al.; length limit: unlimited) Timeout:
Emboss-2.9.0 (rules based on Tuschl et al.; length limit: unlimited) Timeout:
MPI Principles (rules based on Tuschl et al.; length limit: unlimited) Timeout:
GenScript (rules based on Reynolds et al.; length limit: unlimited) Timeout:
Dharmacon (rules based on Tuschl et al., Reynolds et al.; length limit: 10,000bp) Timeout:
Qiagen (rules based on Tuschl et al.; length limit: unlimited) Timeout:
siDirect (rules based on Ui-Tei et al.; length limit: unlimited) Timeout:
Invitrogen (rules based on proprietary algorithm; length limit: unlimited) Timeout:
Deqor (rules based on state-of-the-art parameters; length limit: 5,000bp) Timeout:
MPI + Rational (rules based on Tuschl et al., Reynolds et al.; length limit: unlimited) Timeout:
Filtering of ineffective siRNAs based on secondary structure: (help)
(Details of the filtering mechanism can be found in this paper)
Filtering url (optional, if you have produced the secondary structure using mfold):
Timeout:
No filtering 
Requirements of output siRNAs:
  • Reported by at least software selected above
  • GC content: % - %
  • Minimum position from start codon:
  • Starting nucleotides:
  • Length of siRNA target site:
Delivery of output:
Email:
Online
 

Please sign the guestbook to show your support of our software, and, if possible, share the results of your experiments with other researchers via our database of siRNA.


This website is maintained by Vivien Kwan.
Contributors: TW Lam, Prudence WH Wong, SM Yiu, YC Mui, Vivien Kwan
(Department of Computer Science, The University of Hong Kong)
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