[Bioperl-l] planning sequence mutating modules

Ryan Golhar golharam at umdnj.edu
Tue Feb 14 12:01:38 EST 2006


Here are my two cents....

1.  Allow sequences to be mutated by some percent amount.
2.  Use mutation patterns implied by PAM matrices or some known models
of mutation.
3.  Have the output show the original sequences and the mutated sequence
so you can easily identify what was mutated and what is conserved.

Ryan


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Heikki
Lehvaslaiho
Sent: Tuesday, February 14, 2006 11:09 AM
To: bioperl-l at lists.open-bio.org; Georgii A Bazykin
Subject: Re: [Bioperl-l] planning sequence mutating modules



Yegor,

Like you said, there are examples how it is done.. It should be possible
to 
evolve sequences based on a rooted tree. You just walk the tree and
evolve 
each sequence from its parent.  If there is  an agreement how the branch

lengths get translated to  mutations, even that could be done. Do you
have 
any suggestions?

	-Heikki



On Tuesday 14 February 2006 16:34, Georgii A Bazykin wrote:
> Hi,
>
> Just a thought: I really think that in perspective, it would be nice 
> to be able to evolve the sequence along a tree of given shape. I think

> PAML's "evolver" has this functionality. I've already been doing this 
> in my scripts, but I am not sure how to couple the tree and the 
> sequence data properly.
>
> Yegor (George) Bazykin
>
>
> ------------------------------
>
> Tuesday, February 14, 2006, 1:59:29 AM, you wrote:
> > I've committed an interim solution to the sequence evolution 
> > problem:
> >
> >     $newseq = Bio::SeqUtils-> evolve
> >         ($seq, $similarity, $transition_transversion_rate);
> >
> > I will go on to transform this code to fully OO, extensible 
> > solution.
> >
> >    -Heikki
> >
> > On Friday 10 February 2006 09:06, Heikki Lehvaslaiho wrote:
> >> Ryan Golhar's mail got me thinking that we should have a simple 
> >> framework for mutating sequences to a desired level. The model can 
> >> then be extended to necessary complexity when needed by 
> >> subclassing.
> >>
> >> To start with, I have been planning:
> >>
> >>
> >> Bio::SeqEvolution::EvolutionI - interface file
> >> Bio::SeqEvolution::EvolutionI::seq() - seq to mutate
> >> Bio::SeqEvolution::EvolutionI::seq_type() - returned seq class,
> >>         (defaults to Bio::PrimarySeq)
> >> Bio::SeqEvolution::EvolutionI::next_seq() - overridable by 
> >> subclasses
> >> Bio::SeqEvolution::EvolutionI::each_seqs($count)
> >>        - returns an array of $count seqs
> >> Bio::SeqEvolution::EvolutionI::_generate_seq()
> >> Bio::SeqEvolution::EvolutionI::matrix  # Bio::Matrix::Scoring
> >>       converteed to probabilites of change internally
> >>
> >>   various methods to define the extent of divergence:
> >>   only one to start with:
> >> Bio::SeqEvolution::EvolutionI::pam() -percentage accepted mutation
> >>    (= 100% - identity)
> >>
> >> Bio::SeqEvolution::Factory - core class to call,
> >>          instantiates subclasses, Bio::SeqEvolution::DNASimple for 
> >> nucleotides Bio::SeqEvolution::EvolutionI::type() - evolution
model,
> >>       defaults to Bio::SeqEvolution::DNASimple for nucleotides
> >>
> >>
> >> Bio::SeqEvolution::DNASimple - default for nucleotides 
> >> Bio::SeqEvolution::DNASimple::transversion_rate - positive integer,
> >>         e.g. 5 => 5:1, defaults to 1:1
> >>         simple alternative to a scoring matrix
> >>
> >>
> >> I am soliciting usual comments and suggestions about naming and 
> >> minimal functionality.
> >>
> >>
> >>    -Heikki
>
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-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________
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