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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:

   http://bugzilla.open-bio.org/
 
 

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().