[BiO BB] Blast tree view widget

Mike Marchywka marchywka at hotmail.com
Fri Jun 15 20:31:49 EDT 2007

Did you try asking them? Their general help desk  could probably get you to
developers but they probably have a link somewhere. I've never had a problem
getting info from them on just about anything.

As far as google, try something with the term "visualization" as in "data 
for a start. The clustering search engines always help get me started, try 
vivisimo or
clusty ( can't remember which name is more recent).

FWIW, I went
crazy with openGL for molecule viewing ( not all the features of RasMol
yet, but almost as fast in some modes and nice for custom code trials
like cavity fill- I have some artistic interaction surfaces [ still looking 
for realistic potentials ])
and started to add a general purpose graphing system.
This is kluged right now but amazingly easy to write. My point is that
if you have a c++ compiler you can probably write your own pretty quickly.

Don't underestimate how quickly templatized OO code lets you build up a 
code library either and also don't forget how easy it is to write a one page 
that you can pipe to and from. I have had some experimental distance 
and I could write them in a page of code and tack them onto a "main" method-
then I have something that works with all my scripts. There are always a few
caveats for performance - I ripped out all the ">>" junk for reading fasta 
files in favor of "readsome"
( or whatever the method is for buffer access, I'm away from the code right 
but usually you don't have to track down flakely memory corruption problems 

If you want to move slowly, main(argc argv) works just as a class method as 
it does
at global scope :)

>From: Raja Loganantharaj <logan at cacs.louisiana.edu>
>Reply-To: logan at cacs.louisiana.edu,"General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: "The general forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>Subject: [BiO BB] Blast tree view widget
>Date: Fri, 15 Jun 2007 18:33:08 -0500
>NCBI  has a cool program to display sequence pairwise distances over the 
>WEB. Does anyone know how to get a copy of the widget or how they do it. I 
>guess the input to the widget is a 2x2 distance matrix. Pointer to any 
>other similar program to display nodes using the distance is appreciated. 
>Googling did not help.
>General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org

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