Profile search in GCG

Ramanujam Raman ramjam at scripps.edu
Fri Apr 18 22:42:00 EST 1997

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. 




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