[BiO BB] Global sequence alignments
marchywka at hotmail.com
Mon Feb 19 16:31:20 EST 2007
I'm still using clustalw- I even have scripts to parse the output.
Also, to reply to earlier poster on data interaction, apparently R does have
if it does something close to what
you want it may be realistic to modify the code or make your own contributed
Sorry for lack of alphabetical order but I also downloaded O- has anyone
to model cavities? I couldn't quite figure it out and thought there may be
examples of better suggestions.
I also am surprised how easy it is to do simple things
with openGL ( as per someone's suggestion earlier). It was pretty easy to
a simple atom class, read a pdb file to populate an STL container of atoms,
read a radius
file from the O distribution, and quickly make a solid model similar to
RasMol. The nice
thing about this is that now I can perform operations on the atom
collection, generate a
new collection of pseudo-atoms ( test spheres that fill a cavity for example
) and then display
my calculated "molecule." I'm sure there are packages for this but it
doesn't take long before
you wish the calculations were done in optimized native code- so C++ with
the STL library
and openGL works pretty well.
If you want to try
something like this with a windoze system and no tools, consider downloading
pymol won't build easily but most of these other things will.
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>From: Raj <rajkumar.bondugula at gmail.com>
>Reply-To: "General Forum at Bioinformatics.Org"
><bio_bulletin_board at bioinformatics.org>
>To: bio_bulletin_board at bioinformatics.org
>Subject: [BiO BB] Global sequence alignments
>Date: Fri, 16 Feb 2007 23:11:13 -0600
> Can any one suggest me a downlodable program to perform global
>sequence alignment between two protein sequences and give me their
>sequence identity in percentage?
>Thank you for your time.
>General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org
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