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
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 .