In article <33583F08.4135 at scripps.edu>,
Ramanujam Raman <ramjam at scripps.edu> writes:
> Dear Netters,
> What are the programs in GCG that would allow me to search a protein
> profile against a nucleotide database? [...]
tprofilesearch is an EGCG programme that will do that.
Make sure that EGCG is installed en your machine. Make sure
also that tprofilesearch was compiled with definitions to
scan the whole ESTs (memory limitrations) (contact your GCG manager...).
> 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? [...]
It depends of how it was configured on your system. A general
answer is to make a FOSN with database names. This look like :
Get the names of available databases with gcgver.
Then you can use profilesearch against @my_list_of_DB.
> 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?
Phylip is not a programme, it's a complete package dedicated
to phylogenetic analysis. Remember that this is a complete field
of molecular biology and that using the phylip package (so, doing
good phylogenetic analysis) need some knowledge.
> 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.
For GCG8, Frd compiles an HTML version of the doc. New GCG
licence make it available only for sites where GCG has a valid licence.
(you can contact Fred at : plewniak at igbmc.u-strasbg.fr). GCG9 comes
with its own HTML documentation.
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