mckennalab/FlashFry

support for other PAM sequences

gnapham opened this issue · 7 comments

gnapham commented

Is it possible to add functionality to build the off target database using custom PAM sequences?

aaronmck commented

Hi gnapham,

Totally; this has been requested a couple of times, I'll try to make some headway on this, though it'll take a bit of time. I'll check back when I have something here. Thanks,

Aaron

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charlesfeigin commented

Hi, are there still plans for custom PAM sequences or alternative enzymes?

aaronmck commented

Hi charlesfeigin,

Slow progress on it. Right now the big issue is that we store targets in 48 bits, so we're limited to 24 basepair targets. Version 2 is in the works that will support longer target sequences. If your custom target (+ PAM) is 24 bases or less we can add support for that pretty quickly, but longer targets will require the changes in V2.

-Aaron

jdavnich commented

I'd just like to add my support for the custom target length (especially for Cpf1 - I'm interested in 27nt = 23 + PAM).

Very nice tool by the way.

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alancleary commented

I'd also like to add my support for longer/custom target sequences. @aaronmck, is there an ETA on version 2?

simone-pignotti commented

Hi @aaronmck, any news about this feature? Thanks 🙏

sri-jumpcode commented

Hi @aaronmck, I have been following this issue and it would be absolutely beneficial if Flashfry could have custom PAM sites.

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