BETApro 1.0: Prediction of beta residue pairs, beta strand pairs, strand
alignment, strand pairing direction, and beta-sheet topology 

Reference:
J. Cheng, P. Baldi, Three-Stage Prediction of Protein Beta-Sheets by Neural
Networks, Alignments, and Graph Algorithms,  Proceedings of Intelligent Systems for Molecular
Biology (ISMB 2005), Bioinformatics, vol. 21(Suppl 1), pp. i75-84, 2005. 

Contact:
Paul Rigor
Pierre Baldi
Institute for Genomics and Bioinformatics
Bren School of Information and Computer Sciences
University of California Irvine
email: prigor@ics.uci.edu, pfbaldi@ics.uci.edu


Copyright: 
	The program is free for scientific/academic use. 
	
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Installation (Linux Version):

0. Install SSpro4.0 package first. Get it from: http://download.igb.uci.edu/. Very easy to install. 

1.unzip betapro-1.0.tar.gz
	e.g. tar xzf  betapro-1.0.tar.gz

2.change directory into betapro-1.0 
	e.g. cd betapro-1.0 

3. edit configure.pl
	set installation path (install_dir) and SSpro4 path (pspro_dir) to their installation directories.

4. run configure.pl
	e.g. ./configure.pl

Installation is done!

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Check the integrity of installation using examples

	cd test

	1)make beta residue pairing prediction using the following command:

	../bin/predict_beta_fasta.sh 1vjga.fasta 1vjga.out

	1vjga.out should be same as 1vjga.map. 1vjga.out contains the followiing
	information:
		line1: name; line 2: sequence; line 3: secondary structure
		line 4,5: ignore; the rest of lines: beta-residue pairing probability matrix

	2)predict beta strand pairs and beta strand alignments from
		a beta-residue paring probability matrix:
		../bin/predict_strand.sh 1vjga.out  test 

	The following two files: test.str test.viz will be generated.

		test.str is the prediction of beta-strand pairs, alignment, pairing direction
		and beta-sheet topology. 

		test.viz: is the graph file of beta strand pairings. It can be
		visualized by GraphViz (http://www.graphviz.org/). 

		test.str and test.viz should be the same as 1vjga.str and 1vjga.viz
		respectively. 

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Some scripts in bin directory:

1. predict_beta_fasta.sh

	Predict beta-residue pairing probability matrix from a sequence in
	fasta format. It will use SSpro4 to predict secondary structure first. See
	./test/1vjga.fasta for an example. 
	The sequence in the file should be on one single line.   


2. predict_beta_ss.sh

	Predict beta-residue pairing probability matrix from a sequence with
	user defined secondary structure. See ./test/1vjga_ss for an example.

3. predict_strand.sh

	Predict beta-strand alignment, beta-strand pairings,
	pairing direction, beta-sheet topology from beta-residue pairing probability
	marix.  

4. matrix2png.sh

	Convert beta-residue pairing probability matrix to png image
	file. To do this, you need to install GD library for perl first.  

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You also can access the web server at:
http://www.ics.uci.edu/~baldig/betasheet.html

Enjoy it!