Bio::Prospect -- perl modules for Prospect protein threading
$Name: Release-1-04 $
============================================================

Bio::Prospect:: is an application programmer interface (API) to the
PROSPECT Pro threading application.  The modules provide for program
execution, results parsing, multiple sequence alignments inferred from
pairwise sequence-structure alignments, and rudimentary homology models.

For more information on PROSPECT Pro:
  Kim, D., Xu, D., Guo, J., Ellrott, K. and Xu, Y. (2003) PROSPECT II:
  Protein structure prediction method for genome-scale applications. Protein
  Eng., 16(9), 641-50. Commercial versions available from Bioinformatics
  Solutions, Inc. (http://www.bioinformaticssolutions.com/).

This code is available from CPAN as Bio::Prospect and on SourceForge at
http://www.sf.net/projects/prospect-if/ .


INSTALLATION

Prior to installation 
   Set PROSPECT_PATH and PDB_PATH (if not already set) and make sure that
   mview is in your path prior to running "perl Makefile.PL".

   Makefile.PL will customize the PROSPECT_PATH, PDB_PATH and MVIEW_APP
   variables in Bio/Prospect/Init.pm based on your environment.  It uses
   the PROSPECT_PATH and PDB_PATH environment variables as is, and it will
   search your path for mview to set MVIEW_APP.  "make test" is likely to
   fail if these are not set correctly.

To install this module type the following:
   perl Makefile.PL
   make
   make test
   make install


CONFIGURATION

After installation:
1) verify that all the parameters in the Init module are correctly defined.
2) run the bin/processPdbFiles script to generate processed PDB files.
   These processed files are necessary for generating rudimentary
   backbone-only homology models in PDB format by mapping the aligned
   residues onto the 3D template.  Make sure that you have defined the
   PROSPECT_PATH, PDB_PATH, and PROCESSED_PDB_PATH variables correctly
   within the Bio::Prospect::Init module.

Something akin to this bash command will build all of processed PDB files.
	export PROSPECT_PATH=<top-level of your prospect install>;
	find $PROSPECT_PATH -name \*.xml | 
	sed -e 's/^.*\///;s/\.xml$//' | 
	xargs perl -I ../.. processPdbFiles


DEPENDENCIES
This module requires these other modules and libraries:
- XML::Parser, XML::Simple, Digest::MD5 (available from
   http://www.cpan.org) and bioperl (http://www.bioperl.org).
- For remote threading, SOAP::Lite (http://www.soaplite.com/) and
   SOAP::Transport::HTTP::Daemon (http://www.cpan.org) are required.
- Colorized multiple sequence alignments requires mview
   (http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/).
- Viewing sequence-structure alignments requires rasmol
   (http://www.openrasmol.org/).


AUTHORS
David S. Cavanaugh <cavs@gene.com>
Reece K. Hart <rkh@gene.com>
Genentech, Inc.


FOR MORE INFORMATION
http://share.gene.com/
http://search.cpan.org/~reece/


COPYRIGHT AND LICENCE
Academic Free License 2.0
See the file LICENSE included with this distribution, or view it
online at http://www.opensource.org/licenses/afl-2.0.php .
