MSF as input to plotsimilarity

John Edward Hill HILLJ01 at MCRCR6.MED.NYU.EDU
Sun Nov 27 18:10:55 EST 1994

For GCG8 (and GCG7, as I remember), you can use a msf file from PILEUP,
but you have to use the GCG syntax for indicating which sequences from the
msf file you want.  For example, if you want all the sequences you would

$ plotsimilarity pileup.msf{*}

It's a great way to scan for regions of similarity vs. differences across
the multiple alignment as a whole. 

Good luck!

John Edward Hill, Ph.D.              |  Department of Cell Biology             
Internet: hillj01 at mcrcr.med.nyu.edu  |  New York University Medical Center
  EARN/Bitnet: HILL at NYUMED.BITNET    |  550 First Avenue                  
212-263-7135    FAX: 212-263-8139    |  New York, New York  10016

On Sun, 27 Nov 1994, Brian Foley wrote:

> 	The documentation says that the output created by PILEUP
> (the pileup.msf file) can be used as input to PLOTSIMILARITY.
> 	However, this is not working for me.  PLOTSIM says it cannot
> read pileup.msf.  The documantation also says that all the sequences
> have to be the same length, and my PILEUP was of sequences of
> various lengths, gaps were introduced.  Could this be the problem?
> If so, how does one plot the similarity of proteins that have
> udergone deletions/insertions during evolution?
> --
> ********************************************************************
> *  Brian Foley               *     If we knew what we were doing   *
> *  Molecular Genetics Dept.  *     it wouldn't be called research  *
> *  University of Vermont     *                                     *
> ********************************************************************

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