SVMSEQ for protein residue-residue contact prediction
                         version 1.0 written by Sitao Wu


INSTALL THE SOFTWARE:
1. uncompress SVMSEQ_source.tar.bz2 to a directory like xxxx/SVMSEQ_source.
2. change path settings of xxxx/SVMSEQ_source/library/bin/psipred24/runpsipred:
      dbname=xxxx/SVMSEQ_source/library/data/nr/nr.filter
      ncbiname=xxxx/SVMSEQ_source/library/bin/blast/bin
      execname=xxxx/SVMSEQ_source/library/bin/psipred24/bin
      dataname=xxxx/SVMSEQ_source/library/bin/psipred24/data
3. change the setting of xxxx/SVMSEQ_source/SVMSEQ/SVMSEQ.pl:
      
      $datadir="xxxx/SVMSEQ_source/example/$pdb"; #contact predictions are saved in 
	                                          # "xxxx/SVMSEQ_source/example/$pdb"
      $libdir="xxxx/SVMSEQ_source/library"; #SVMSEQ libary
      $bindir="xxxx/SVMSEQ_source/library/bin"; # Directory of SVMSEQ executalbe files
      $user="username"; # Your user name
    
HOW TO RUN THE SOFTWARE:
Suppose the sequence file is saved in xxxx/SVMSEQ_source/example/e01/seq.txt. First 
change current directory to xxxx/SVMSEQ_source/SVMSEQ. Then type:
"./SVMSEQ.pl e01".
After the prediction is finished, contact predictions are saved in
"xxxx/SVMSEQ_source/example/$pdb/svmseq.dat" respectively.


All questions to stwu@ku.edu
12/17/2008

Reference:
S. Wu, Y. Zhang. A comprehensive assessment of sequence-based and template-based methods
for protein contact prediction. Bioinformatics, vol 24, 924-931 (2008).