README for MCPrimers.pm V1.5.1, mcprimers.pl, and CloningVector.pm

1. Authorship and copyright

Author:    Stephen G. Lenk, November 2005, May 2006.
Copyright: Stephen G. Lenk (C) 2005, 2006. All rights reserved. 

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

############################################################################
# This software comes with no guarantee of usefulness.
# Use at your own risk.
# 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.
############################################################################

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
CloningVector.pm - Place into Bio/Data/Plasmid/CloningVector.pm
mcprimers.pl     - Front end script. Make available to users.

PRIMER3DIR -   Set this environment variable to point to diectory containing
               Primer3 executable.

If PRIMER3DIR is not set, MCPrimers will set it to '.' by default.

MSWindows -    use primer3.exe
Other OS  -    use primer3_core

3. Purpose

Creates molecular cloning PCR primer pairs for a given gene so that the
gene can be directionally inserted into a vector. pET-32a is the only
vector currently supported. Solver is generic, restriction enzymes and 
their order in the vector are specified in mcprimer.pl and in 
CloningVector.pm

4. Use

Use:     perl mcprimers.pl [options] -vector name dna.fasta > result.pr3
Options: [-h] [-shift search_shift] [-clamp (both | 3prime)]

-h        help
-vector   cloning vector name (i.e. pET-32a)
-shift    integer value to shift search of left RE match into gene
          use -shift 12 (or other value) if initial search fails
-clamp    GC clamp
          'both' will clamp last NT at both ends to G or C (default)
          '3prime' will clamp last NT on 3' ends to G or C
          
Example:  

perl mcprimers.pl -vector pET-32a -shift 12 -clamp 3prime ppib.fa > ppib_all.pr3

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

Limitations: Does not account for redundancy codes in FASTA files.

Note:        These runs use intermediate files. This means that
             CGI or other use that can overwrite these files is
             a bad idea. 

5. Test Results (1.5.1)

Passes test.pl clean on Windows XP with Activestate Perl
OSX with non-Activestate Perl there are different results each time from mcprimers !?
Not tested on Linux

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

Enjoy,

Steve Lenk
slenk@emich.edu
May 2006