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 <email@example.com> Reece K. Hart <firstname.lastname@example.org> 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 .