Bio::Tools::Run::PiseApplication::eprimer3(3)

NAME
Bio::Tools::Run::PiseApplication::eprimer3

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::eprimer3

      Bioperl class for:

        EPRIMER3        Picks PCR primers and hybridization oligos (EMBOSS)

      Parameters:

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/eprimer3.html
         for available values):

                eprimer3 (String)

                init (String)

                sequence (Sequence)
                        sequence -- dna [sequences] (-sequence)
                        pipe: seqsfile

                explainflag (Switch)
                        Explain flag (-explainflag)

                fileflag (Switch)
                        Create results files for each sequence (-fileflag)

                task (Excl)
                        Select task -- Task (-task)

                numreturn (Integer)
                        Number of results to return (-numreturn)

                firstbaseindex (Integer)
                        First base index (-firstbaseindex)

                includedregion (Integer)
                        Included region(s) (-includedregion)

                target (Integer)
                        Target region(s) (-target)

                excludedregion (Integer)
                        Excluded region(s) (-excludedregion)

                forwardinput (String)
                        Forward input primer sequence to check (-forwardinput)

                reverseinput (String)
                        Reverse input primer sequence to check (-reverseinput)

                pickanyway (Switch)
                        Pick anyway (-pickanyway)

                mispriminglibrary (InFile)
                        Mispriming library (-mispriminglibrary)

                maxmispriming (Float)
                        Primer maximum mispriming (-maxmispriming)

                pairmaxmispriming (Float)
                        Primer pair maximum mispriming (-pairmaxmispriming)

                gcclamp (Integer)
                        GC clamp (-gcclamp)

                osize (Integer)
                        Primer optimum size (-osize)

                minsize (Integer)
                        Primer minimum size (-minsize)

                maxsize (Integer)
                        Primer maximum size (-maxsize)

                otm (Float)
                        Primer optimum Tm (-otm)

                mintm (Float)
                        Primer minimum Tm (-mintm)

                maxtm (Float)
                        Primer maximum Tm (-maxtm)

                maxdifftm (Float)
                        Maximum difference in Tm of primers (-maxdifftm)

                ogcpercent (Float)
                        Primer optimum GC percent (-ogcpercent)

                mingc (Float)
                        Primer minimum GC percent (-mingc)

                maxgc (Float)
                        Primer maximum GC percent (-maxgc)

                saltconc (Float)
                        Salt concentration (mM) (-saltconc)

                dnaconc (Float)
                        DNA concentration (nM) (-dnaconc)

                numnsaccepted (Integer)
                        Maximum Ns accepted in a primer (-numnsaccepted)

                selfany (Float)
                        Maximum self complementarity (-selfany)

                selfend (Float)
                        Maximum 3' self complementarity (-selfend)

                maxpolyx (Integer)
                        Maximum polynucleotide repeat (-maxpolyx)

                productosize (Integer)
                        Product optimum size (-productosize)

                productsizerange (Integer)
                        Product size range (-productsizerange)

                productotm (Float)
                        Product optimum Tm (-productotm)

                productmintm (Float)
                        Product minimum Tm (-productmintm)

                productmaxtm (Float)
                        Product maximum Tm (-productmaxtm)

                maxendstability (Float)
                        Maximum 3' end stability (-maxendstability)

                oligoexcludedregion (Integer)
                        Internal oligo excluded region (-oligoexcludedregion)

                oligoinput (String)
                        Internal oligo input sequence (if any) (-oligoinput)

                oligoosize (Integer)
                        Internal oligo optimum size (-oligoosize)

                oligominsize (Integer)
                        Internal oligo minimum size (-oligominsize)

                oligomaxsize (Integer)
                        Internal oligo maximum size (-oligomaxsize)

                oligootm (Float)
                        Internal oligo optimum Tm (-oligootm)

                oligomintm (Float)
                        Internal oligo minimum Tm (-oligomintm)

                oligomaxtm (Float)
                        Internal oligo maximum Tm (-oligomaxtm)

                oligoogcpercent (Float)
                        Internal oligo optimum GC percent (-oligoogcpercent)

                oligomingc (Float)
                        Internal oligo minimum GC (-oligomingc)

                oligomaxgc (Float)
                        Internal oligo maximum GC (-oligomaxgc)

                oligosaltconc (Float)
                        Internal oligo salt concentration (mM) (-oligosaltconc)

                oligodnaconc (Float)
                        Internal oligo DNA concentration (nM) (-oligodnaconc)

                oligoselfany (Float)
                        Internal oligo maximum self complementarity (-oligoselfany)

                oligoselfend (Float)
                        Internal oligo maximum 3' self complementarity (-oligoselfend)

                oligomaxpolyx (Integer)
                        Internal oligo maximum polynucleotide repeat (-oligomaxpolyx)

                oligomishyblibrary (InFile)
                        Internal oligo mishybridizing library (-oligomishyblibrary)

                oligomaxmishyb (Float)
                        Internal oligo maximum mishybridization (-oligomaxmishyb)

                outfile (OutFile)
                        outfile (-outfile)

                auto (String)

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 the Bioperl mailing list. Your participation is much appreciated.

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

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

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

AUTHOR
Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT
Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

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

DISCLAIMER
This software is provided "as is" without warranty of any kind.

SEE ALSO

•   http://bioweb.pasteur.fr/seqanal/interfaces/eprimer3.html

•   Bio::Tools::Run::PiseApplication

•   Bio::Tools::Run::AnalysisFactory::Pise

•   Bio::Tools::Run::PiseJob

  new
 Title   : new()
 Usage   : my $eprimer3 = Bio::Tools::Run::PiseApplication::eprimer3->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::eprimer3 object.
           This method should not be used directly, but rather by
           a Bio::Tools::Run::AnalysisFactory::Pise instance.
           my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
           my $eprimer3 = $factory->program('eprimer3');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::eprimer3.