[BiO BB] Global sequence alignments

Mike Marchywka 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 
source code-
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 
used this
to model cavities? I couldn't quite figure it out and thought there may be 
some good
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.

( note new address as of 10-06)
Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165r
404-788-1216 (C)<- leave message
989-348-4796 (P)<- emergency only

>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
>Hello all,
>      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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