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
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 | "You are never given a wish
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The Scripps Research Institute | the power to make it true;
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Off.: (619) 784-2220 |
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email: ram at scripps.edu |