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