Bio::SeqEvolution::DNAPoint(3pm)			User Contributed Perl Documentation			  Bio::SeqEvolution::DNAPoint(3pm)

NAME

       Bio::SeqEvolution::DNAPoint - evolve a sequence by point mutations

SYNOPSIS

	 # $seq is a Bio::PrimarySeqI to mutate
	 $evolve = Bio::SeqEvolution::Factory->new (-rate => 5,
						    -seq => $seq,
						    -identity => 50
						    );
	 $newseq = $evolve->next_seq;

DESCRIPTION

       Bio::SeqEvolution::DNAPoint implements the simplest evolution model: nucleotides change by point mutations, only. Transition/transversion
       rate of the change, rate(), can be set.

       The new sequences are named with the id of the reference sequence added with a running number. Placing a new sequence into a factory to be
       evolved resets that counter. It can also be called directly with reset_sequence_counter.

       The default sequence type returned is Bio::PrimarySeq. This can be changed to any Bio::PrimarySeqI compliant sequence class.

       Internally the probability of the change of one nucleotide is mapped to scale from 0 to 100. The probability of the transition occupies
       range from 0 to some value. The remaining range is divided equally among the two transversion nucleotides. A random number is then
       generated to pick up one change.

       Not that the default transition/transversion rate, 1:1, leads to observed transition/transversion ratio of 1:2 simply because there is only
       one transition nucleotide versus two transversion nucleotides.

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/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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

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

AUTHOR

	 Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt>

CONTRIBUTORS

       Additional contributor's names and emails here

APPENDIX

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

   seq
	Title	: seq
	Usage	: $obj->seq($newval)
	Function: Set the sequence object for the original sequence
	Returns : The sequence object
	Args	: newvalue (optional)

       Setting this will reset mutation and generated mutation counters.

   set_mutated_seq
	 Title	 : seq_mutated_seq
	 Usage	 : $obj->set_mutated_seq($newval)
	 Function: In case of mutating a sequence with multiple evolvers, this
	 Returns : set_mutated_seq
	 Args	 : newvalue (optional)

   rate
	 Title	 : rate
	 Usage	 : $obj->rate($newval)
	 Function: Set the transition/transversion rate.
	 Returns : value of rate
	 Args	 : newvalue (optional)

       Transition/transversion ratio is an observed attribute of an sequence comparison. We are dealing here with the transition/transversion rate
       that we set for our model of sequence evolution.

       Note that we are using standard nucleotide alphabet and that there can there is only one transition versus two possible transversions. Rate
       2 is needed to have an observed transition/transversion ratio of 1.

   next_seq
	 Title	 : next_seq
	 Usage	 : $obj->next_seq
	 Function: Evolve the reference sequence to desired level
	 Returns : A new sequence object mutated from the reference sequence
	 Args	 : -

   mutate
	 Title	 : mutate
	 Usage	 : $obj->mutate
	 Function: mutate the sequence at the given location according to the model
	 Returns : true
	 Args	 : integer, start location of the mutation, required argument

       Called from next_seq().

perl v5.14.2							    2012-03-02					  Bio::SeqEvolution::DNAPoint(3pm)