Welcome to DSIR

DSIR is a tool for siRNA (19 or 21 nt) and shRNA target design. It implements an algorithm based on the following publication: Vert JP, Foveau N, Lajaunie C, Vandenbrouck Y. An accurate and interpretable model for siRNA efficacy prediction.BMC Bioinformatics. 2006 Nov 30;7(1):520. Recently a comparison study based on four independent siRNA datasets ranked DSIR as one of the best predictors among several programs evaluated [Matveeva et al., 2007]
Sequence to target
First, name your design session and then enter your target sequence. You can either use the input field by simply copy-paste your sequence or upload a sequence fasta file. In both cases, your sequence has to respect the FASTA format (or DSIR will throw an error).

Design name :  * required
Sequence :
 (FASTA format only) 
or upload file :
Prediction settings
The first analysis performed by DSIR is the prediction of the efficacy of all possible siRNAs targeting your input sequence. The efficacy (or score) computed by DSIR is based on a linear model that combines siRNA and target sequence features.

RNA design : siRNA 19nt  siRNA 21nt  shRNA
Score threshold :  
Filter 4 or more nucleotide runs : Yes  No
Avoid immunostimulatory motifs : Yes  No