Subject: Snake plot program - round 2

From: Jan Torleif Pedersen <JATP_at_Lundbeck.com>
Date: Wed, 11 Feb 2004 09:37:53 +0100

Greetings again,

And thanks for all the input on the snake plotting program. So three options
fell out of the survey, none of which were really satisfying so it appears
that there is scope for a nice tool here.

The result of the query was:

1) Viseur by  Champagne
http://icbtools.med.cornell.edu/viseur/overview.html
Development of this seems to have stopped - am I right ?
Does not appear to make snake plots in an intelligent way, long
intracellular loops result in a three page postscript file with the insert.
Also does not remove alignment gaps when making the snake plot.

2) The SOSUI tool 
http://sosui.proteome.bio.tuat.ac.jp/sosuiframe0.html
This is a web-based tool and can not be used for proprietary sequences.

3) Use a molecular modelling program and make a nice ribbon drawing.
Ahhh well that is an option but the cartoons do have some pedagogical
advantages.

Any other ideas are welcome. Or if anybody has a few lines of code that
generate a PostScript that would be appreciated.

		Regards    -- Jan

Dr. Jan Torleif Pedersen
Section head, Bioinformatics
Department of Molecular Genetics
H. Lundbeck A/S
Ottiliavej 9, 2500 DK-Valby
Denmark
phone: +45 36 43 28 87
FAX: +45 36 43 82 53
email: jatp_at_lundbeck.com

---

From: "Fabien Campagne" <fac2003[at]med.cornell.edu>
Date: Wed, 11 Feb 2004 15:31:07 -0500

Greetings,

The development of Viseur has stopped in 1998. I agree that the
algorithm that Viseur used to build snake-plots is by today's standards
a bit primitive. See [3] for a different and more flexible method.

If you are interested in snake-plots, please check out the Residue-based
Diagram editor:

http://icb.med.cornell.edu/crt/RbDe/Rbde.xml [1]

(This is a web-based application)

For batch processing of snake-plots and other residue-based diagrams,
please see our Residue-based Diagram Generator, RbDg:

http://icb.med.cornell.edu/crt/RbDg/index.xml [2]

These two tools are actively developed and maintained. Free academic
licenses are offered. Nonexclusive site-licenses are available for
industry through the Cornell Research Foundation. Contact me directly if
you are interested. I am not a CCL subscriber. 

[1] Skrabanek L, Campagne F, Weinstein H. Building protein diagrams on
the web with the residue-based diagram editor RbDe.
Nucleic Acids Res. 2003 Jul 1;31(13):3856-8. 

[2] Campagne F, Bettler E, Vriend G, Weinstein H. Batch mode generation
of residue-based diagrams of proteins.
Bioinformatics. 2003 Sep 22;19(14):1854-5. 

[3] Campagne F, Weinstein H. Schematic representation of residue-based
protein context-dependent data: an application to transmembrane
proteins.
J Mol Graph Model. 1999 Jun-Aug;17(3-4):207-13. 

Fabien Campagne, PhD -- http://icb.med.cornell.edu
Bioinformatics Officer, Institute for Computational Biomedicine
Assistant Professor,    Dept. of Physiology and Biophysics

Weill Medical College of Cornell University ----------------------
phone: (212)-327-8341   c/o Rockefeller University, Smith Hall 410
fax:   (212)-327-7344   Box 270; 1230 York Avenue
----------------------- New York, NY 10021 -----------------------

-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request[at]ccl.net] On
Behalf Of Jan Torleif Pedersen
Sent: Wednesday, February 11, 2004 3:38 AM
To: 'chemistry[at]ccl.net'
Subject: CCL:Snake plot program - round 2

Greetings again,

And thanks for all the input on the snake plotting program. So three
options
fell out of the survey, none of which were really satisfying so it
appears
that there is scope for a nice tool here.

1) Viseur by  Campagne
intracellular loops result in a three page postscript file with the
insert.

2) The SOSUI tool 

		Regards    -- Jan

Dr. Jan Torleif Pedersen
Section head, Bioinformatics
Department of Molecular Genetics
H. Lundbeck A/S
Ottiliavej 9, 2500 DK-Valby
Denmark
phone: +45 36 43 28 87
FAX: +45 36 43 82 53
email: jatp[at]lundbeck.com

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