siRNA Design Software

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.