Thursday, July 14, 2016

DAPPLE 2 -- Homology-based PTM searches!

Some people out there aren't studying lab strains yeast or E.coli or nematodes of even ridiculously inbred mice. These weirdos are studying these things cause they cause diseases or just cause we don't know anything about them. A consequence of this aberrant behavior can be that their organism of interest hasn't been sequence (or...realistically at this point....sequenced, but not annotated). Think it is tough to assign the correct phosphorylation site to yeast? Try assigning it in an extremophile that somebody did a crappy next gen sequencing run on.

DAPPLE 2 is an attempt to help these people out and is a topic of this new paper in JPR. Why is it DAPPLE 2? Maybe cause if you just look for "Dapple" you just get these...

!!!!!  ERMAHGERD!!!!  The 2 is important -- unless you want to waste your pre-work coffee time flipping through puppy pictures rather than blogging...

I didn't finish this?  Actually, DAPPLE is an algorithm that has already existed. DAPPLE 2 is an improvement on this approach. DAPPLE2 draws on post translational motifs from 15 different databases.

Despite drawing on all of these resources it still ends up as FASTER than the original algorithm in their datasets!

If you're thinking "Great...another phosphorylation motif search tool..." I say to you -- ever heard of malonylation? I haven't!  It is one of the many PTM motifs that this tool can search. While most of the data out there is phosphorylation (for good reason) this group didn't forget that it is just one important PTM and there are other ones that might be what's up with your organism!  (Looks like there are at least 20 different PTMs in their table!)

Seriously a nice resource!  Want to check it out directly? Here is the link (did I mention it is web-based?!)

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