Wednesday, March 29, 2017

ProtVista -- Visualize all the protein information!

As we continue to pile new genome and protein sequences into all these databases we have to come up with something better than just text sequences. You could argue that the few graphical sequence tools out there could use a refresh as well.

I'm happy to see that people are actively working on this stuff! Proof is in this extremely short open access paper in Bioinformatics!

It details this new visualization tool, what resources it uses, where to download it and the source code but the coolest info in the paper (to me, anyway!) is that it is already in use by multiple tools we all already use!

To verify I went after a protein I studied for a while, typed it into Uniprot -- and BOOM!

Once you find the protein (and correct species) click the accession ID then click Feature Viewer and you get the ProtVista results! This isn't just colorful, it's super useful. For example, if you click on PTMs, it expands and you get all these little symbols

Hover over them and it gives you a little box that shows what the modification is and who has verified it. Check out the disulfide bond row (column? whatever...)!! How ridiculously valuable is that if you are really characterizing this protein in depth? I'll tell you. Very ridiculously valuable.

If this isn't enough for ProtVista, you can go directly to the page and get the software for yourself -- with instructions -- and source code here!

Minor aside here -- While looking for this tool, I discovered UniProt hosts a surprisingly useful YouTube page. Seriously, I normally just go to UniProt and bumble around looking for FASTAs and click lots of things till I find them. I was vaguely aware they were adding lots of cool tools to it (and maybe always had some) but I'd stolen my Zip files and ran away.

There is a lot of cool stuff here and these videos will show you what they are. Maybe even more useful? There are really basic intro videos you can send to customers or collaborators if they're outside the field and ask you what a "FASTer" is!  ;)

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