README FOR BETA-HELIX PREDICTION PROGRAM:

Download the file betawrap.tar.gz from www.cs.columbia.edu/~abk2001/compgen/betawrap.tar.gz

Run the following commands:
>gunzip betawrap.tar.gz
>tar -xvf betawrap.tar

The following file should be present in a folder called betawrap/
betawrap_latest.pl: The main program
bur.dat: buried residue score matrix
exp.dat: exposed residue score matrix
errs
neg_err
negativeTestResults: results on all negative test set proteins
positiveTestResults: results on all positive test set proteins
runnegative: script to test all negative test set proteins
runpositive: script to test all positive test set proteins
pred2ary.jar: the alpha helix predictor
and two directories
positiveTest/ : the positive test set
negativeTest/ : the negative test set

The negativeTest/ has 2 more directories
alpha_nonbhelix/ : all negative test set alpha proteins
beta_nonbhelix/  : all negative test set beta proteins

NOTE: All files were tested on LINUX machines
NOTE: All protein files must be in FASTA format.
NOTE: A JAVA compiler and a PERL interpreter is required

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NOTE: Please set your path correctly to your java/bin directory in the program betawrap_latest.pl (line 490). By default it is considered to be usr/java/bin
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To run the program on a single file
>./betawrap_latest.pl <path/filename>

e.g.
>./betawrap_latest.pl positiveTest/2pec

To run the program on individual files
To run the scripts the commands are:
>./runpositive > positiveTestResults
>./runnegative > negativeTestResults

to print the results to the files
and
>./runpositive
>./runnegative

to print it out on the screen