
############################################################################
SVMcon is a software to predict protein residue-residue contacts in 8
Angstrom distance threshold.
It is one of the most accurate contact predictors in the 7th edition
of Critical Assessment of Techniques for Protein Structure Prediction (CASP7).
It is the only free contact map prediction software (including source code)
available so far. 

Reference: 
J. Cheng and P. Baldi. Improved Residue Contact Prediction Using Support Vector Machines
and a Large Feature Set. BMC Bioinformatics. 8:113, 2007. 

Author: Jianlin Cheng, PhD. School of EECS, University of Central Florida. 

Free for academic and scientific use only.
Copyright @ Jianlin Cheng
Please do not re-distribute the software without the permission of the author.

Contact: 
Jianlin Cheng at jianlin.cheng@gmail.com

############################################################################

Third-party software used by SVMcon

SVMcon softwre uses svm_classify program in SVM-light
(svmlight.joachims.org) to classify data points.

Reference to SVM-light:

T. Joachims, 11 in: Making large-Scale SVM Learning Practical. Advances in
Kernel Methods - Support Vector Learning, B. Schölkopf and C. Burges and A.
Smola (ed.), MIT Press, 1999. 

I thank the author of SVM-light (Dr. Thorsten Joachims) for the permit
to include svm_classify in the SVMcon package

Here is the license quoted from the SVM-light website:

SVM-light is free only for non-commercial use. It must not be distributed
without prior permission of the author. The author is not responsible for
implications from the use of this software.

#############################################################################

Installation

1. install secondary structure and solvent accessibility predictor SSpro4 
   (download it from: contact.ics.uci.edu/download.html. easy to install)

2. unzip svmcon.tar.gz 

3. do configuration

	cd svmcon
	open configure.pl
	set $install_dir to svmcon directory
	set $pspro_dir to SSpro4 directory (full path)
	save configure.pl
	run ./configure.pl to configure.

installation is done.

------------------------------------------------------------------------------------

Test Installation

cd test
../bin/predict_map.sh T0288.fasta test.map   

The output test.map should be the same as T0288.map.final

------------------------------------------------------------------------------------

Run the program:

	predict_map.sh fasta_file output_file

	fasta_file: protein sequence in the simple FASTA foramt 
	(line1: >name; line 2: a plain protein sequence). 

	Output file includes the predicted residue contacts in CASP format.

Notice:
	Since there are lot of support vectors in the SVM model, it takes from
	tens of minutes to several hours to predict contacts for a protein, depending
	on sequence length. 
------------------------------------------------------------------------------------

