PROSPECT Version 2.0: Introduction Installation Quick Guide Running Prospect Manager Input Formats Templates Parameters Configurations Outputs References FAQ

Prospect Manager ProspectManager is a perl script that utilizes Perl/Tk to allow the user to interface with the standard Prospect tools in a GUI interface.  It can be found in the bin directory of the prospect installization. It can be called by the command: prospect_manager.pl You set the sequence file to work with, and the basic options, such as which database to thread aginst, the number of CPUs to use, and the type of threading to be used. There are a number of envirormental varibles that need to be set up in order for Prospect Manager to correctly find the tools that it needs.  These enviromental varibles can be setup in the shell initialization script, or in the entry lines in Prospect Manager after the program has been launched. The main window The following need to be set for Prospect Manager to work correctly: PROSPECT_PATH - The is the path to the base of the Propspect install, all prospect related tools need this enviromental varible in order to find the prospect databases. BLASTPGP_EXE - The path of blastpgp, so that sequence profiles can be generated BLASTPGP_DB - This is the path to the database you'll search with Blastpgp, typically, the Non-redundent database is a good start. MODELLER_EXE - You will need to set this if you intened to use Prospect alignments for Modeller input RASMOL_EXE - Set this so you can view any generated PDB files. PVM_ARCH - This tells Prospect Manager which binary to call.  The naming scheme for the binaries <program name>.$PVM_ARCH.   On i686 Linux machines, PVM_ARCH is 'LINUX', on Sun Machines  it is 'SUN4SOL2', LinuxPPC machines it is 'LINUXPPC', on alpha Machines it is 'ALPHA', and on MacOSX it is 'DARWIN'. Upon pressing the 'Run Prospect Tools' button, Prospect Manager goes through a set series of commands, namely: Running blast to generate a sequence profile Predicting the secondary structure Running prospect Sorting the results, and then displaying them in a window for user interface Note, if you've already ran the prospect tools before, and wish to re-open the results file, press 'Open Prospect Results' Sorted results