Introduction:
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OligoWalk -  calculates themodynamic features of sense-antisense hybidization. 
	It predicts the free energy changes of oligonucleotide binding to a target RNA.
siRNAWalk.pl - is a perl script to run OligoWalk and predict siRNA automatically.
	You need to install perl and libsvm to have siRNAWalk.pl running


Prerequisite:
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LIBSVM: 
	Download LIBSVM, compile it and copy svm-predict svm-scale to directory svm/.
	LIBSVM is avilable at: http://www.csie.ntu.edu.tw/~cjlin/libsvm/
	Its use should be cited as: Chih-Chung Chang and Chih-Jen Lin, 
		LIBSVM : a library for support vector machines, 2001. 
		Software available at http://www.csie.ntu.edu.tw/~cjlin/libsvm


Installation:
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Go to directory src/, then type:
	'make OligoWalk' to make the excutable OligoWalk in exe/

	'make clean' can be used to remove the object files
	'make realclean' can be used to removethe executables for rebuilding


Usage:
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To predict efficient siRNA (using the siRNAWalk.pl script):
	1. Go to the root directory of OligoWalk (oligowalk_src)
	2. Please type in the name of your sequence file and an options file like
 		./siRNAWalk.pl example.seq [example.options]

Sequence file format:
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Input sequences are in the .seq format.  example.seq provides an example.  At the start
of the file, lines beginning with ";" denote comments.  There needs to be at least one comment line.
The following line has a sequence title. 
The following lines are the sequence, with whitespace ignored.  The sequence terminates with a '1' 
character.  

Options:
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See example.options for a list of available options.


Outputs:
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example.siRNA:  siRNA candidates
example.energy: free energy table of each binding site on the target, it includes:

position:       5' end of the target site
overall:        overall free energe change of the equilibrium 
duplex:         free energy change of the sense-antisense hybrid duplex
breaking:       the free energy cost to open the binding site's base pairs
Tm:             melting temperature of sensen-antisense duplex
intraoligo:     free energy change of intra-oligomer structure
interoligo:     free energy change of inter-oligomer (antisense dimer) structure
end_diff:       the difference of the free enegy change of the two ends of siRNA duplex (5' end - 3'
 endwindow size: 2)
sequence:       the sequence of antisense siRNA (5'-3')


SVM for siRNA prediction:
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There two svm files for siRNA prediction:
svm/svm_model:   used for folding size of 800nt (whole length if less than 800nt); folding method is partition function calculation
svm/svm_scaler:   used for scale inputs for svm before running svm-predict


REFERENCE:
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Zhi John Lu and David H. Mathews. 2008.  Efficient siRNA selection using hybridization thermodynamics. 
	Nucleic Acids Research, 36: 640-647.

QUESTIONS:
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Please send questions to David Mathews:
	David_Mathews@urmc.rochester.edu .




