Thursday, January 8, 2015


Click on the picture above to expand it.  Its awesome.

Do you know about the "next gen" sequencing method called Ribo-Seq?  Me neither. Thanks to the magic that is Wikipedia, I now know a little bit about it.  Apparently it figures out the messenger RNAs that are present at a given point in time.  With that information we get a snapshot of what the cell is saying to translate.  Cool, right?  Sound hoaxy?  Sure!  I'll ask a genomics expert about it later.

But genomics labs are generating this data. The first paper Wikipedia cites is from 2009, so that info is out there.

This is where PROTEOFORMER comes in.  This pipeline takes that information and translates it into the protein sequence information.  Then you can search that information with a variety of tools available through Peptide Shaker and SearchGUI.  If this Ribo-Seq thing says its present and the MS/MS confirms it, I'd say that Ribo-Seq thing isn't a bad idea!

You can check out PROTEOFORMER at its website here.
You can read the original paper from J. Crappe et. al., here.

Thanks go to Pastel BioSciences for leading me to this great resource!

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