Protocol Online logo
Top : New Forum Archives (2009-): : siRNA, microRNA and RNAi

si-Fi, Software for RNAi off-target prediction - (Oct/06/2009 )


Iím pleased to announce si-Fi 1.2beta - our new Software for RNAi (RNA interference) off-target prediction.
The software is designed for checking long-double stranded RNAi constructs for target specificity and silencing efficiency. It can be used also for selecting sequences regions suitable for designing RNAi constructs for specific and efficient silencing of genes. The program provides clear tabular and graphical outputs.
Simply paste your RNAi trigger sequence and check it for targets and off-targets within your local sequence database (unigene sets for many species can be downloaded free of charge from the specialized online databases). Unlike the online tools, si-Fi uses a local sequence database that gives you a full control over it. Any sequence database in a multiple Fasta format can be imported with few mouse clicks only.
You are kindly invited to test the Beta version of si-Fi by downloading it from:
This is open source software which can be considered as a gift to the community. It can be used and distributed free of charge.
Any comments and suggestions are welcome. Please sent it to

Kind regards


We have a new version of si-Fi containing a major improvement. The software is no longer BLAST based! Instead we switched to an algorithm called Bowtie. BLAST was only a temporary solution, and we knew that it isn't perfect. It often fails to find all hits and it's kind of unpredictable. Bowtie is by far more reliable in finding siRNA matches and it's as fast as BLAST. So, new improved version is available for downloading at:

Comments are welcome!


si-Fi has now an official homepage:

Kind regards,