Profile search in GCG

Stuart M. Brown browns02 at mcrcr0.med.nyu.edu
Tue Apr 22 09:52:59 EST 1997

In article <33583F08.4135 at scripps.edu>, Ramanujam Raman
<ramjam at scripps.edu> wrote:

> Dear Netters,
> I am a beginner in using GCG programs.  I am trying to do some alignment 
> and do some database search for that alignment. I use pileup to do my
> alignment and use the resulting MSF output to generate a profile.
> What are the programs in GCG that would allow me to search a protein
> profile against a nucleotide database?  I have a profile from a seried
> of protein sequences (aligned with pileup).  Using this profile, I would
> like to search a nucleotide database like ESTs.  What I need is
> something similar to tblastn in BLAST.  Can this be done using a profile
> in GCG?   
> For now I have tried to scan it against protein databases.  Is there
> one  designation in the command-line that would let me scan all the
> protein databases?  I tried using p:*, protein:*, GP:*, GPA:* and all 
> the times, it searches only a particular protein subset.  What should I
> type in for a overall search of all protein databases? 
> Also, what are the best programs to use to generate phylogenetic trees? 
> I have been using the distance matrix and then run the output through
> the Growtree function.  Is distance matrix the best way to look for
> divergence or similarity?  Is the Phylip program any different or better
> with regard to phylogenetic analysis? 
> Finally, where would I find a good documentation for GCG?  As a 
> beginner, I find the accompanying manual for the program under
> informative!  I very much appreciate any reply for all or any of the
> above.  I may even be completely missing or unaware of the simplest of
> solution. So please email any suggestions you have and I would also be
> glad to give more information if need. Reply to my email address. 

> RAMANUJAM RAMAN                |        
> Department of Cell Biology     | 

These are some excellent questions - by my standards you are hardly a
beginner. If you are looking for some general background and tutorials
on GCG, I have put my entire bioinformatics course on-line at 

Stuart M. Brown, Molecular Biology Consultant 
NYU-MC Research Computing Resource, Dept. of Cell Biology
550 First Ave, New York, NY 10016
Phone: (212)263-7689  FAX: (212)263-8139

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