[vineetg]

(Author of the blog post here)

We use the scoring function published by Hsu et al[1], which most scientists seem to be using. This function takes into account both the number of mismatches and where they occur in the guide. There's a more readable version here: http://crispr.mit.edu/about .

[1] http://www.nature.com/nbt/journal/v31/n9/full/nbt.2647.html

[danieltillett]

Interesting that indels are not considered. We found that with RNA/DNA hybridisation that the probes with indels bind with high efficiency [1].

1. http://www.ncbi.nlm.nih.gov/pubmed/20649647