Viewing profile — vineetg

Original author here. Thanks for the kind words! We would love open source some of the work we did - there are a few edge cases to still work out with deprecated_column and renamed…

Original author here. You're right - conceptually the CRISPR search problem and DNA sequence alignment are related. In both, you're looking for place where two (or more) sequences …

I briefly mentioned it in the "New Infrastructure" section, but we're doing the splitting and combining of results on our web servers.

We're getting around 100ms connection times. We're using the Node aws-sdk to get things from S3: s3.getObject({Bucket, Key})

EBS costs are actually fairly small ($9 a month per instance for 90GB). More than 95% of our costs were just paying for the EC2 servers.

We actually do this in our "expensive" check. The reason that we use the 2 arrays is because in 2 array lookups, we can check for matches for all 200 guides. I probably could've ma…

A lot of these are actually pretty easy to spot with tools like gcov. To determine false positives, we can just look at how many times each "if" statement was hit, and compare thos…

Thanks for bringing up all of these alternatives. We definitely would have preferred to use an existing solution to building our own. Unfortunately, a lot of the existing software …

We messed around with bowtie - it seems like most of these are optimized for the number of alignments being small (i.e. close to 1). Unfortunately, the number of matches for a 20 b…

I left PAM sites out of the blog post (it's actually mentioned briefly in the footnotes), as it made the problem slightly more complicated. The final algorithm actually keeps track…

(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 mi…