primer3_core(1) [debian man page]

PRIMER3_CORE(1) 					       Primer3 User Manuals						   PRIMER3_CORE(1)

NAME

       primer3_core - Designs primers for PCR

SYNOPSIS

       primer3_core [-format_output] [-strict_tags] [< input_file]

DESCRIPTION

       primer3_core picks primers for PCR reactions, considering as criteria oligonucleotide melting temperature, size, GC content and
       primer-dimer possibilities, PCR product size, positional constraints within the source sequence, and miscellaneous other constraints.

       By default, primer3_core accepts input and produces output in Boulder-io format, a pre-XML text-based input/output format for
       program-to-program data interchange format. The Boulder-io format and the commands that primer3_core understands are described in the
       README file, which on Debian systems can be found in /usr/share/doc/primer3/.

OPTIONS

       -format_output
	   Prints a more user-oriented report for each sequence.

       -strict_tags
	   primer3_core echoes and ignores any tags it does not recognize, unless the -strict_tags flag is set on the command line, in which case
	   primer3_core prints an error in the PRIMER_ERROR output tag, and prints additional information on stdout; this option can be useful for
	   debugging systems that incorporate primer.

       Note
       The old flag -2x_compat is no longer supported.

EXIT STATUS CODES

       o   0 on normal operation.

       o   -1 under the following conditions: illegal command-line arguments, unable to fflush stdout, unable to open (for writing and creating) a
	   .for, .rev or .int file (probably due to a protection problem).

       o   -2 on out-of-memory.

       o   -3 empty input.

       o   -4 error in a "Global" input tag (message in PRIMER_ERROR).

REFERENCE

       Please cite Rozen, S., Skaletsky, H. "Primer3 on the WWW for general users and for biologist programmers." In S. Krawetz and S. Misener,
       eds. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology. Humana Press, Totowa, NJ, 2000, pages 365-386.

SEE ALSO

       ntdpal(1) oligotm(1)

COPYRIGHT

       Copyright (C) 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen
       (http://jura.wi.mit.edu/rozen), Helen Skaletsky

       All rights reserved. On Debian-based systems, please consult /usr/share/doc/primer3/copyright to read the licence of primer3_core.

       This manual page was written by Steffen Moeller <moeller@debian.org> for the Debian(TM) system (but may be used by others). Permission is
       granted to copy, distribute and/or modify this document under the same terms as primer3_core itself.

primer3_core 1.1.4						    05/09/2008							   PRIMER3_CORE(1)

Bio::Tools::Run::Primer3(3pm)				User Contributed Perl Documentation			     Bio::Tools::Run::Primer3(3pm)

NAME

       Bio::Tools::Run::Primer3 - Create input for and work with the output from the program primer3

SYNOPSIS

       Bio::Tools::Primer3 creates the input files needed to design primers using primer3 and provides mechanisms to access data in the primer3
       output files.

       This module provides a bioperl interface to the program primer3. See http://frodo.wi.mit.edu/primer3/primer3_code.html for details and to
       download the software. This module only works for primer3 release 1 but is not guaranteed to work with earlier versions.

	 # design some primers.
	 # the output will be put into temp.out
	 use Bio::Tools::Run::Primer3;
	 use Bio::SeqIO;

	 my $seqio = Bio::SeqIO->new(-file=>'data/dna1.fa');
	 my $seq = $seqio->next_seq;
	 my $primer3 = Bio::Tools::Run::Primer3->new(-seq => $seq,
						     -outfile => "temp.out",
						     -path => "/usr/bin/primer3_core");

	 # or after the fact you can change the program_name
	 $primer3->program_name('my_suprefast_primer3');

	 unless ($primer3->executable) {
	   print STDERR "primer3 can not be found. Is it installed?
";
	   exit(-1)
	 }

	 # what are the arguments, and what do they mean?
	 my $args = $primer3->arguments;

	 print "ARGUMENT	MEANING
";
	 foreach my $key (keys %{$args}) {print "$key	", $$args{$key}, "
"}

	 # set the maximum and minimum Tm of the primer
	 $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);

	 # design the primers. This runs primer3 and returns a
	 # Bio::Tools::Run::Primer3 object with the results
	 $results = $primer3->run;

	 # see the Bio::Tools::Run::Primer3 pod for
	 # things that you can get from this. For example:

	 print "There were ", $results->number_of_results, " primers
";

       Bio::Tools::Run::Primer3 creates the input files needed to design primers using primer3 and provides mechanisms to access data in the
       primer3 output files.

       This module provides a bioperl interface to the program primer3. See http://www-genome.wi.mit.edu/genome_software/other/primer3.html for
       details and to download the software.

       This module is based on one written by Chad Matsalla (bioinformatics1@dieselwurks.com). I have ripped some of his code, and added a lot of
       my own. I hope he is not mad at me!

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://www.bioperl.org/MailList.html		  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 http://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Rob Edwards

       redwards@utmem.edu

       Based heavily on work of Chad Matsalla

       bioinformatics1@dieselwurks.com

CONTRIBUTORS

       Shawn Hoon shawnh-at-stanford.edu Jason Stajich jason-at-bioperl.org Brian Osborne osborne1-at-optonline.net

SEE ALSO

       Bio::Tools::Primer3

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new()
	Title	: new()
	Usage	: my $primer3 = Bio::Tools::Run::Primer3->new(-file=>$file) to read
		  a primer3 output file.
		  my $primer3 = Bio::Tools::Run::Primer3->new(-seq=>sequence object)
		  design primers against sequence
	Function: Start primer3 working and adds a sequence. At the moment it
		  will not clear out the old sequence, but I suppose it should.
	Returns : Does not return anything. If called with a filename will allow
		  you to retrieve the results
	Args	: -seq (optional) Bio::Seq object of sequence. This is required
		  to run primer3 but can be added later with add_targets()
		       -outfile file name to output results to (can also be added
		  with $primer3->outfile_name
		       -path path to primer3 executable, including program name, e.g.
		  "/usr/bin/primer3_core". This can also be set with program_name
		  and program_dir
		       -verbose (optional) set verbose output
	Notes	:

   program_name
	Title	: program_name
	Usage	: $primer3->program_name()
	Function: holds the program name
	Returns:  string
	Args	: None

   program_dir
	Title	: program_dir
	Usage	: $primer3->program_dir($dir)
	Function: returns the program directory, which may also be obtained from ENV variable.
	Returns :  string
	Args	:

   add_targets()
	Title	: add_targets()
	Usage	: $primer3->add_targets(key=>value)
	Function: Add any legal value to the input command line.
	Returns : Returns the number of arguments added.
	Args	: Use $primer3->arguments to find a list of all the values
		  that are allowed, or see the primer3 docs.
	Notes	: This will only do limited error checking at the moment,
		  but it should work.

   run()
	Title	: run()
	Usage	: $primer3->run();
	Function: Run the primer3 program with the arguments that you have supplied.
	Returns : A Bio::Tools::Primer3 object containing the results.
	Args	: None.
	Note	: See the Bio::Tools::Primer3 documentation for those functions.

   arguments()
	Title	: arguments()
	Usage	: $hashref = $primer3->arguments();
	Function: Describes the options that you can set through Bio::Tools::Run::Primer3,
		  with a brief (one line) description of what they are and their
		  default values
	Returns : A string (if an argument is supplied) or a reference to a hash.
	Args	: If supplied with an argument will return a string of its
		  description.
		  If no arguments are supplied, will return all the arguments as a
		  reference to a hash
	Notes	: Much of this is taken from the primer3 README file, and you should
		  read that file for a more detailed description.

   version
	Title	: version
	Usage	: $v = $prog->version();
	Function: Determine the version number of the program
	Example :
	Returns : float or undef
	Args	: none

   _input_args()
	Title	: _input_args()
	Usage	: an internal method to set the input arguments for Primer3
	Function: Define a hash with keys for each of the input arguments and values
		  as a short one line description
	Returns : A reference to a hash.
	Args	: None.
	Notes	: Much of this is taken from the primer3 README file, and you should
		  read that file for a more detailed description.

perl v5.12.3							    2011-06-18					     Bio::Tools::Run::Primer3(3pm)