Introducing an optimized score for sgRNA design

Roger Pellegrini

When designing sgRNAs, selecting an sgRNA that can cleave your targeted genomic region effectively (i.e. high on-target activity) is very important. How can you predict which sgRNAs are most likely to work well for your experiments?


Benchling just released an optimized scoring tool that Doench, Fusi et al. described in Nature Biotechnology early this year. This optimized score has more predictive power than the previous on-target score Doench et al. developed in 2014. You can learn more about how they optimized the algorithm here.

Benchling has been working hard to make the optimized score for our users. We are very excited that now you can use the score in Benchling to optimize your guide selection.

Let’s take a look!

How do you use the improved sgRNA scoring method in Benchling

In Benchling, the default is to use the previous on-target score for sgRNA design. However, it is very easy to start using the new optimized score.

In the dialog to set guide parameters, click “Advanced Settings”:


Then check the box “Use Optimized Score from Doench, Fusi et al. (2016)”:


You will then see the optimized score associated with each sgRNA. The score is from 0 to 100. The higher the better.



That’s it! Now you can use the optimized score to select the best sgRNAs for your experiments. Please let us know if you have any feedback or suggestions!

Curious about how Doench, Fusi et al. developed the optimized score? Check out this post to learn more about the science behind the metric.

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