Monday, May 1, 2017

ShettiMotif -- Find conserved protein regions!

Now for something completely different - and kinda brilliant! 

ShettiMotif is a data mining tool that searches FASTA and FLAT (please pardon capitalization) files for linear structural motifs.

Who cares?

Maybe lots of people -- but definitely virus researchers! To show the usefulness of their program, this group searches the protein structural information of 11 viruses and finds that there are a lot of similarly expressed proteins in viruses that infect the same kinds of cells.

I'm imagining what I could do with the opposite. Now that I know that these 20 or so protein motifs are found the most often in viruses that can infect cell type A and I've now got a 12th virus, can I predict from the protein information whether the virus would infect cell A? Doesn't seem like much of a stretch!

Closer to my knowledge base, malaria parasites produce cell surface proteins with extensive variable regions (the level to which these proteins can change is comparable to the level our own antibodies can class switch!) and it looks like I could visually compare motifs between different proteomes if I get them into their own files and formatted correctly.  There are probably lots of other uses for this really nice interface (it is simple to install and use, just download the Zip file and run the .EXE) that I don't have the imagination to think of. There are loads of pre-curated motifs already loaded too!

The output is graphical and surprisingly intuitive.

To try this for yourself and your cool project you can download ShettiMotif here! 

1 comment:

  1. Hi Ben! This is a bit of a long shot but do you still have the zip file for ShettiMotif? It's pretty much perfect for my project but the download link is broken and I can't get in contact with Haitham Sobhy.
    Thank you so much!