This web service does NOT run BLAST searches to find possible matches in untargeted genes. Please check the uniquenessof your siRNA candidates by BLAST against the transcriptome of the organism!
This algorithm has been trained and validated on mammalian sequences and on the following cell lines: HeLa,NCI-H1299, and HEK293 using Lipofectamine and/or Oligofectamine transfection maintained at a level of 95 percent transfection. Knockdown was measured 24 hours after transfection.

Although we believe that the ranking of the target sites could be similar, the actual activity of the siRNAs may differ from the predicted one in different species, cell lines,experimental conditions, and transfection agents.

Please upload or paste a SINGLE targeted mRNA in FASTA-format.
You may want to mask the nonunique parts of the sequence by "N" characters.

FASTA Upload

Enter a name for your sequence:

Upload your sfold SSTRAND output file in text format for the same mRNA for the assessment of the accessibility oftarget loci. You can run predictions without sfold data at somewhat lower accuracy.

You can obtain sfold output files by submitting your sequence to

Please cite:
Istvan Ladunga:
More Complete Gene Silencing by Fewer siRNAs: Transparent Optimized Design and Biophysical Signature
Nucleic Acids Res.2007;35(2):433-440.