README for MCPrimers.pm V2.3, mcprimers.pl, mcprimers_gui.pl,
and CloningVector.pm

1. Authorship and copyright

Authors:   MCPrimers:     Stephen G. Lenk, 2005, 2006.
           CloningVector: Tim Wiggin and Steve Lenk 2006
           
Copyright: Stephen G. Lenk (C) 2005, 2006 on MCPrimers.pm
           Tim Wiggin and Steve Lenk (C) 2006 on CloningVector.pm

This program is free software; you can redistribute it and/or  
modify it under the same terms as Perl itself.
Licenced under the Perl Artistic Licence.

############################################################################
# This software comes with no guarantee of usefulness.
# There is no guarantee this code will find the best solution, or even 
# any solution, or that the solutions it finds will be correct or useful 
# to you.
#
# Use at your risk. Check any solutions you obtain.
#
# Stephen G. Lenk assumes no responsibility for the use of this software.
# Tim Wiggin assumes no responsibility for the use of this software.
#
############################################################################

Primer3 is called by this code to verify that the PCR primers are OK.
Primer3 is Copyright (c) 1996,1997,1998,1999,2000,2001,2004
Whitehead Institute for Biomedical Research. All rights reserved.

2. Installation

MCPrimers.pm     - Place into Bio/MCPrimers.pm
                   Use the perl site directory for Activestate
CloningVector.pm - Place into Bio/Data/Plasmid/CloningVector.pm
                   Use the perl site directory for Activestate

mcprimers.pl     - Front end CLI script. Make available to users.
mcprimers_gui.pl - GUI. Make available to users.

You WILL want to wrap the .pl files with a shell script or batch file
so that the environment variables can be set. Remember that pl2bat
on XP (Activestate) will make a batch file. You can edit the resulting
file and add environment variables. Example files are provided.

pET-32a.txt   - Put in data dir.
                It is OK to make your own vector data files.

MCPRIMER_DIR  - Set this environment variable to point to the directory 
                containing mcprimers.pl                   
PRIMER3_DIR   - Set this environment variable to point to the directory 
                containing the Primer3 executable.

MCPrimers defaults environment variables to its starting directory.

mcprimers.acd - provided for EMBOSS users

MSWindows - use primer3.exe
Other OS  - use primer3_core

It is easiest to test and install mcprimers.pl & modules first
then test and install the GUI.

Note: Use perl -Ilib if modules are still in local lib directory.

3. Purpose

Creates molecular cloning PCR primer pairs for a given gene so that the
gene can be directionally inserted into a vector, which is defined in
an external data file.

Solver is generic, restriction enzymes and their order in the vector 
are specified in the data file specified.

4. Test Results (V2.3)

t/test.pl will test the release when run from a command line

Passes test.pl clean on Windows XP with Activestate Perl 5.8.7
Passes test.pl clean on OSX with Activestate Perl 5.8.8
Passes test.pl clean on Linux with the standard installed Perl 5.8.7 

On OSX with non-Activestate Perl (5.8.1) there are different 
results each time mcprimers is run, so ... use Activestate Perl!

The GUI was tested (OK) on XP and OSX.

mcprimers.acd was checked on XP with acdc.exe and acdverify.exe

---------------

Enjoy,

Steve Lenk
slenk@emich.edu