Saturday, May 25, 2013

Compass -- Awesome tools from the Coon lab

I needed to write this one: 1) To lead into my upcoming monologue on False Discovery Rates.  And 2) Because I use this all the time and somehow I've never written about it.

If you are not familiar, you should be.  COMPASS is a set of free tools from the Coon lab.  It can do all of the things shown above.  I use and underutilize this all the time.  Because what I use it for is to build FASTA files for me.  This is the easiest, fastest way to build a FASTA and get yourself a decoy database.  It'll make you a separate decoy.  It'll append your decoy to the end or your normal FASTA and, as for decoys, it will make you a reverse on, it'll make a scrambled one, and I think it will make a reverse and scrambled one.

If you don't have COMPASS, you should spend the 20 seconds it takes to download it and the 10 minutes it takes to learn to use it.  It is described in this paper from 201l, and you can download it here.

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