Sunday, April 29, 2018

Prot-SpaM -- Fast alignment of PROTEOMES for phylogeny reconstruction

It is really hard to type this because the picture is just cracking me up. Focus, Ben. Stop laughing.


The genomics people do things like this all the time -- take the DNA sequences and figure out how everyone is related to whom. Prot-SpaM allows us to jump in and look at the phylogeny of organisms (alignment free) from the protein sequences. 

The results look seriously cool when they come out of the software but you have to zoom in like 100 times to tell that you aren't just looking at a weird smear on the page.

Those are compressed circular dendrograms!!  How cool is that?

Now here is the neat thing about this -- classically this stuff is ALWAYS done with gene alignments (essentially permutations on just BLASTing the entire genomes of organisms). This requires supercomputer level resources. Prot-SpaMming doesn't. It requires far less resources AND (this makes sense to us protein people) protein sequence information appears to be a far more sensitive method for detecting relation than DNA alignment. Wins all around!


  1. The paper is now published in GigaScience:

  2. The Prot-SpaM paper has now been published in its final form in the OUP journal GigaScience: