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.\"
.IX Title "Bio::SeqEvolution::DNAPoint 3pm"
.TH Bio::SeqEvolution::DNAPoint 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
Bio::SeqEvolution::DNAPoint \- evolve a sequence by point mutations
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 6
\&  # $seq is a Bio::PrimarySeqI to mutate
\&  $evolve = Bio::SeqEvolution::Factory\->new (\-rate => 5,
\&                                             \-seq => $seq,
\&                                             \-identity => 50
\&                                             );
\&  $newseq = $evolve\->next_seq;
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Bio::SeqEvolution::DNAPoint implements the simplest evolution model:
nucleotides change by point mutations, only. Transition/transversion
rate of the change, \fIrate()\fR, can be set.
.PP
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.
.PP
The default sequence type returned is Bio::PrimarySeq. This can be
changed to any Bio::PrimarySeqI compliant sequence class.
.PP
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.
.PP
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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
.Vb 1
\&  Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt>
.Ve
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Additional contributor's names and emails here
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "seq"
.IX Subsection "seq"
.Vb 5
\& Title   : seq
\& Usage   : $obj\->seq($newval)
\& Function: Set the sequence object for the original sequence
\& Returns : The sequence object
\& Args    : newvalue (optional)
.Ve
.PP
Setting this will reset mutation and generated mutation counters.
.SS "set_mutated_seq"
.IX Subsection "set_mutated_seq"
.Vb 5
\&  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)
.Ve
.SS "rate"
.IX Subsection "rate"
.Vb 5
\&  Title   : rate
\&  Usage   : $obj\->rate($newval)
\&  Function: Set the transition/transversion rate.
\&  Returns : value of rate
\&  Args    : newvalue (optional)
.Ve
.PP
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.
.PP
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.
.SS "next_seq"
.IX Subsection "next_seq"
.Vb 5
\&  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    : \-
.Ve
.SS "mutate"
.IX Subsection "mutate"
.Vb 5
\&  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
.Ve
.PP
Called from \fInext_seq()\fR.