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Bio::Tools::AmpliconSeUser(Contributed Perl DocumBio::Tools::AmpliconSearch(3)

NAME
       Bio::Tools::AmpliconSearch - Find amplicons in a	template using
       degenerate PCR primers

SYNOPSIS
	  use Bio::PrimarySeq;
	  use Bio::Tools::AmpliconSearch;

	  my $template = Bio::PrimarySeq->new(
	     -seq => 'aaaaaCCCCaaaaaaaaaaTTTTTTaaaaaCCACaaaaaTTTTTTaaaaaaaaaa',
	  );
	  my $fwd_primer = Bio::PrimarySeq->new(
	     -seq => 'CCNC',
	  );
	  my $rev_primer = Bio::PrimarySeq->new(
	     -seq => 'AAAAA',
	  );

	  my $search = Bio::Tools::AmpliconSearch->new(
	     -template	 => $template,
	     -fwd_primer => $fwd_primer,
	     -rev_primer => $rev_primer,
	  );

	  while	(my $amplicon =	$search->next_amplicon)	{
	     print "Found amplicon at position ".$amplicon->start.'..'.$amplicon->end.":\n";
	     print $amplicon->seq->seq."\n\n";
	  }

	  # Now	change the template (but you could change the primers instead) and look
	  # for	amplicons again

	  $template = Bio::PrimarySeq->new(
	     -seq => 'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa',
	  );
	  $search->template($template);

	  while	(my $amplicon =	$search->next_amplicon)	{
	     print "Found amplicon at position ".$amplicon->start.'..'.$amplicon->end.":\n";
	     print $amplicon->seq->seq."\n\n";
	  }

DESCRIPTION
       Perform an in silico PCR	reaction, i.e. search for amplicons in a given
       template	sequence using the specified degenerate	primer.

       The template sequence is	a sequence object, e.g.	Bio::Seq, and the
       primers can be a	sequence or a Bio::SeqFeature::Primer object and
       contain ambiguous residues as defined in	the IUPAC conventions. The
       primer sequences	are converted into regular expressions using
       Bio::Tools::IUPAC and the matching regions of the template sequence,
       i.e. the	amplicons, are returned	as Bio::Seq::PrimedSeq objects.

       AmpliconSearch will look	for amplicons on both strands (forward and
       reverse-	complement) of the specified template sequence.	If the reverse
       primer is not provided, an amplicon will	be returned and	span a match
       of the forward primer to	the end	of the template. Similarly, when no
       forward primer is given,	match from the beginning of the	template
       sequence. When several amplicons	overlap, only the shortest one to more
       accurately represent the	biases of PCR. Future improvements may include
       modelling the effects of	the number of PCR cycles or temperature	on the
       PCR products.

TODO
       Future improvements may include:

       o   Allowing a small number of primer mismatches

       o   Reporting all amplicons, including overlapping ones

       o   Putting a limit on the length of amplicons, in accordance with the
	   processivity	of the polymerase used

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://bioperl.org/wiki/Mailing_lists	- 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:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR
       Florent Angly <florent.angly@gmail.com>

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

   new
	Title	 : new
	Usage	 : my $search =	Bio::Tools::AmpliconSearch->new( );
	Function : Initialize an amplicon search
	Args	 : -template	   Sequence object for the template sequence. This object
				   will	be converted to	Bio::Seq if needed in since features
				   (amplicons and primers) will	be added to this object.
		   -fwd_primer	   A sequence object representing the forward primer
		   -rev_primer	   A sequence object representing the reverse primer
		   -primer_file	   Read	primers	from a sequence	file. It replaces
				   -fwd_primer and -rev_primer (optional)
		   -attach_primers Whether or not to attach primers to Amplicon	objects. Default: 0 (off)
	Returns	 : A Bio::Tools::AmpliconSearch	object

   template
	Title	 : template
	Usage	 : my $template	= $search->template;
	Function : Get/set the template	sequence. Setting a new	template resets	any
		   search in progress.
	Args	 : Optional Bio::Seq object
	Returns	 : A Bio::Seq object

   fwd_primer
	Title	 : fwd_primer
	Usage	 : my $primer =	$search->fwd_primer;
	Function : Get/set the forward primer. Setting a new forward primer resets any
		   search in progress.
	Args	 : Optional sequence object or primer object or	'' to match beginning
		   of sequence.
	Returns	 : A sequence object or	primer object or undef

   rev_primer
	Title	 : rev_primer
	Usage	 : my $primer =	$search->rev_primer;
	Function : Get/set the reverse primer. Setting a new reverse primer resets any
		   search in progress.
	Args	 : Optional sequence object or primer object or	'' to match end	of
		   sequence.
	Returns	 : A sequence object or	primer object or undef

   primer_file
	Title	 : primer_file
	Usage	 : my ($fwd, $rev) = $search->primer_file;
	Function : Get/set a sequence file to read the primer from. The	first sequence
		   must	be the forward primer, and the second is the optional reverse
		   primer. After reading the file, the primers are set using fwd_primer()
		   and rev_primer() and	returned.
	Args	 : Sequence file
	Returns	 : Array containing forward and	reverse	primers	as sequence objects.

   attach_primers
	Title	 : attach_primers
	Usage	 : my $attached	= $search->attach_primers;
	Function : Get/set whether or not to attach primer objects to the amplicon
		   objects.
	Args	 : Optional integer (1 for yes,	0 for no)
	Returns	 : Integer (1 for yes, 0 for no)

   next_amplicon
	Title	 : next_amplicon
	Usage	 : my $amplicon	= $search->next_amplicon;
	Function : Get the next	amplicon
	Args	 : None
	Returns	 : A Bio::SeqFeature::Amplicon object

   annotate_template
	Title	 : annotate_template
	Usage	 : my $template	= $search->annotate_template;
	Function : Search for all amplicons and	attach them to the template.
		   This	is equivalent to running:
		      while (my	$amplicon = $self->next_amplicon) {
			 # do something
		      }
		      my $annotated = $self->template;
	Args	 : None
	Returns	 : A Bio::Seq object with attached Bio::SeqFeature::Amplicons (and
		   Bio::SeqFeature::Primers if you set -attach_primers to 1).

perl v5.24.1			  2017-07-08	 Bio::Tools::AmpliconSearch(3)

NAME | SYNOPSIS | DESCRIPTION | TODO | FEEDBACK | AUTHOR | APPENDIX

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