Wednesday, May 27, 2015

GalaxyP revisit

This week I was lucky enough to spend a few days working with a great group of researchers at various University of Minnesota campuses.  It was all sorts of fun because of the expertise around in the area of bioinformatics and the vendor neutral nature of the institution.  I probably learned as much as anyone in the room.

One reason I was excited for the trip was the chance to revisit one of my favorite posters from ASMS last year.  This poster showed a great workflow for integrating proteogenomics data with the use of the GalaxyP resources (here!)

While the publicly available GalaxyP interface doesn't have the power that the user's at UMinn have internally, it is steadily growing.  If you haven't visited this interface before (or in a while) you should probably check it out.

Here are some highlights:

Raw data conversion resources (online! w00t!)

FASTA merging with data redundancy removal! (the mechanism looks for full sequence homology within FASTA entries and drops anything that matches up to the first one it sees.  Useful to me, for sure!)

Access to proteogenomics tools for converting nucleic acid data to protein sequences.

What they currently have internally that hasn't been implemented outside of UMinn is even more exciting...such as the ability to blast peptide sequences to aid in the identification of new and novel proteoforms.

If you are in Saint Louis next week I suggest you swing by Pratik Jagtap's poster detailing the progress of this package.

And if you happen to be in London around July 6th this year, you should drop in on the Galaxy user's meeting.  Galaxy is a HUGE project with developers around the globe trying to simplify genomics - and now proteogenomics - for the rest of us.

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