[Bioperl-l] Tool to mutate DNA sequence

Heikki Lehvaslaiho heikki at sanbi.ac.za
Thu Feb 9 06:31:20 EST 2006


Ryan,

Instructions in pseudo code:

take the sequence string out of the object
use a hash to store changed locations
repeat 
    pick a location in the string randomly
    if the location is not in a hash , i.e. changed already, 
        change it into something else
    add the changed location into the hash
    if enough locations have been changed (scalar keys hash), exit loop
put the sequence string back into the seq object

   -Heikki   

On Thursday 09 February 2006 06:46, Ryan Golhar wrote:
> Does anyone know of tool to mutate a DNA sequence by a specified amount?
> For instance, say I have a DNA sequence 1000 bases long, and I want to
> simulate mutations to make it 75% (or 80%, etc) similar to the original.
>
>
> Ryan
>
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> Bioperl-l at lists.open-bio.org
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-- 
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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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