Re: secondary structure analysis

From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Fri Jan 11 2013 - 02:57:26 CST

> I know that stride computes this data, but I'm not sure where its
> stored, or how to access it in a script.

Recent versions of carma can produce a file containing secondary structure
assignments from stride (you'll need an executable named 'stride' in the
path (and a linux machine)). The file will look like this (one line per
frame, one char per residue) :

            GGGGGGGGGHTT TTTTTTTTTTTTT
          TTGGGGGGGGGTTT TTTTTTTTTTGGG
          TTGGGTTTGGGTTT TTTTTTTGGG
         TTTGGGGGGGGGTTT TTTTTTTGGG
          TTGGGGGGGGGGTTTT TTTTTTTGGG
            GGGGG GGGGTTTT TTTTTTTGGG
...............

-- 
            Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

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