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://github.com/bioperl/bioperl-live/issues
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().