##
## The files and data in this directory is related to the publication:
##
##  "Quantifying cross-reactive antibody binding and inferring epitopes among 
##   Borrelia burgdorferi OspC variants using protein microarray data" 
##  BMC Bioinformatics, 2013
##  Elisabeth Baum, Arlo Randall, Michael Zeller, Pierre Baldi and Alan G. Barbour
##
## 

################################################################################
Directory: /TerminiScanning/
 
 This directory contains the Perl script and data files necessary to generate
 the results presented in Figure 1 of the article. The script also returns the
 correlation between the global sequence identity matrix and the cross-reactivity
 matrix.


 File: terminiScanning.pl
 
   This is a perl script that takes the multiple sequence alignment file and the 
   raw antibody measuresments as input and produces the correlation results for
   each possible. The header ofthe script contains additional documentation.
   
   Usage:
     "perl terminiScanning.pl <msa_file> <raw_data_file>"
    
    
################################################################################
Directory: /SequenceScanningFullMatrix/
 
 This directory contains the Perl scripts and data files necessary to generate
 the results presented in Figure X of the article. 
 
 File: sequenceScanningFullMatrix.pl

   This is a perl script that implements the method
   This method is described in section 2.6.1 of the article and the results
   are presented in section 3.X.X.


################################################################################
Directory: /FigureGeneration/
 
 This directory contains files and UCSF Chimera commands files to generate the 
 structural images in the publication.
 
 UCSF Chimera can be downloaded for free from: http://www.cgl.ucsf.edu/chimera/


 File: 1GGQ_AB.pdb
 
   The file contains subunits A and B only of the Protein Data Bank entry 1GGQ. 
   These two subunits represent the native dimer of OspC type A. 
   
   This structure file is used with Figure3.cmd
   
 File: Figure3.cmd
 
   The file contains UCSF Chimera commands to generate the view of the OspC
   dimer that appears in Figure 3 of the article.


 File: OspC_consensus_model.pdb
 
   The file contains subunits A and B only of a model of the consensus sequence
   calculated from all 23 OspC types.
   
   This structure file is used with Figure4_A_I3.cmd and Figure4_F_I3.cmd
   
 File: Figure4_A_I3.cmd
  
   The file contains UCSF Chimera commands to generate the view of the OspC
   dimer that appears in the left side of Figure 4 of the article showing 
   the matches and mismatches between OspC types A and I3.

 File: Figure4_F_I3.cmd
  
   The file contains UCSF Chimera commands to generate the view of the OspC
   dimer that appears in the left side of Figure 4 of the article showing 
   the matches and mismatches between OspC types F and I3.