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Stephen G. Lenk > Bio-MCPrimers-2.5 > Bio::MCPrimers



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Module Version: 2.5   Source  




Creates molecular cloning PCR primer pairs for a given gene so that the gene can be directionally inserted into a vector. Solver is generic, restriction enzymes and their order in the vector are specified in the caller.


sub find_mc_primers

    $orf,            # ATGC string (I use 21 NT upstream, 200 NT downsteam)
    $flag_hr,        # anonymous hash reference to flags from
    $pr3_hr,         # hash reference to Primer3 Boulder file tags
    $ecut_loc_ar,    # enzyme cut location array reference from caller
    $vcut_loc_ar,    # vector cut location array reference from caller
    @re              # array of restriction enzyme strings from caller

Not explicitily exported. Use Bio::MCPrimers::find_mc_primers

See for an example of use and front-end.

INSTALLATION ^     - Place into lib/Bio/ - Place into lib/Bio/Data/Plasmid/
    Vector files     - Make vector file directory accessable     - Place in a directory where it can be accessed - Place in a directory where it can be accessed 
    mcprimers.acd    - Put in acd directory for EMBOSS 
                       Only checked with acdvalidate 
    MCPrimers_manual.doc    - User documentation
    MCPRIMER_DIR     - Set this environment variable to point to the 
                       directory containing  
    PRIMER3_DIR      - Set environment variable to point to Primer3 
                       executable directory.
    MSWindows - use primer3.exe
    Other     - use primer3_core


Primer3 used as primer3.exe on MSWindows and as primer3_core otherwise.

Used by, which is used by


Used by


SYNOPSIS ^ -help -vectorfile pet-32a.txt cyss.fa cyss.pr3

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

See for an example of the use of Bio::MCPrimers itself See MCPrimers_manual.doc for user documentation

Note: is a command line program is a GUI on top of


See MCPrimers_manual.doc

Note: Runs use intermediate files keyed to PID.


Probably. Use at your own risk.

This software comes with no guarantee of usefulness. Use at your own risk. Check any solutions you obtain. Stephen G. Lenk assumes no responsibility for the use of this software.


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.

Primer3 is Copyright (c) 1996,1997,1998,1999,2000,2001,2004 Whitehead Institute for Biomedical Research. All rights reserved.

CloningVector (C) Tim Wiggin and Steve lenk 2006


Stephen G. Lenk, November 2005, 2006.


Primer3 is called by this code to verify that the PCR primers are OK.

Thanks to Tim Wiggin for good ideas at the start. Tim rewrote in 2006

Thanks to Dan Clemans for showing me molecular cloning in the first place. I am using Dr. Clemans's ideas about good MC primers in this code. Any errors in interpretation or implementation are mine.

Patricia Sinawe found that earlier versions of MCPrimers did not detect out-of-frame solutions and suggested that extra binding sites could be included.

Ken Youens-Clark has provided guidance in the proper naming of this software so that it functions cooperatively with other Perl modules.

Anar Khan and Alastair Kerr for their advice at BOSC 2006 regarding EMBOSS compatability, Primer3 parameters, and selective use of sites. They also insisted that I enhance MCPrimers to do eukaryotic organisms.

Other references:



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