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#######  README  #######
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The data and software distributed with this file are licensed under
the Academic Free License version 2.1 

See section entitled "License" for full details of the license.
 

OB-Score Calculation Software Copyright (2006) Ian M. Overton, Geoffrey J. Barton and The University of Dundee 

If using this software, data, (or any derivative works) please cite:
Overton, I. M. & Barton, G. J. (2006). "A Normalised Scale for Structural
Genomics Target Ranking: The OB-Score". FEBS Lett. 580:4005-9.

** DEPENDANCIES  **
- BioPerl (edit BEGIN loop of OB.pm to include the PATH to 
your installation of BioPerl)

To report bugs etc. please contact:
ian@compbio.dundee.ac.uk or geoff@compbio.dundee.ac.uk

TEST EXAMPLES (run from directory OB/)

(1)  Run OB.pl in standard mode 
'perl OB.pl -i test_in.fasta -o out.dat -p Hydrophobicity_scores.dat -m zmat.dat'
 
(2) Run OB.pl without calculation of molecular weight 
'perl OB.pl -i test_in.fasta -o out_noMW.dat -n -p Hydrophobicity_scores.dat
 -m zmat.dat'

Example output is given in the files:
example_out.dat  
example_out_noMW.dat

Note:
Using the -n flag output prevents calculation of molecular weight as the 
code (Bioperl) to calculate MW produces error messages if the input contains
non-standard amino acids. In any case, OB.pl never uses MW for calculating
the OB-Score - MW is included simply for additional information.


'perl OB.pl' gives help message (below)

Version 1.0
This software calculates the OB-Score for each sequence in the input fasta file.

OB.pl Output format(tab-delimited):
id      OB-Score        GRAVY   pI      mol_wt(lower_bound)     sequence_length

Abbreviations:
id = sequence identifier
GRAVY = GRand AVerage of hYdrophobicity (defaults to Kyte-Doolittle)
pI = isoelectric point

Command-line input:
 -i [Inputfile (fasta format)]
 -o [output file]
 -p [hydropathy score table] (can use Hydrophobicity_scores.dat)
 -m [score matrix] (use zmat.dat)
 -n no mol_wt calculation (in case of nonstandard amino acids in input)
        output format: id       OB-Score        GRAVY   pI      sequence_length
 -h prints this message

If using this software, data, (or any derivative works) please cite:
Overton, I. M. & Barton, G. J. (2006). "A Normalised Scale for Structural
Genomics Target Ranking: The OB-Score". FEBS Lett. 580:4005-9.


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