[Bioperl-l] Tool to mutate DNA sequence

Heikki Lehvaslaiho heikki at sanbi.ac.za
Thu Feb 9 09:54:30 EST 2006


Ryan,

I should have made this very clear in my first reply:

You have to plan very carefully what rules you use when you mutate your 
sequence because it will affect directly the resulting sequences. Of course,  
all that depends on what you will be using the sequences for. If you are 
going to draw evolutionary conclusions from those sequences, you must mutate 
them in a way that simulates evolutionary principles.

My earlier pseudocode example, for example, should allow mutations in every 
location. Mutations do occur multiple times in same places as sequences get 
saturated by mutations. Also, you should decide the relative occurrence of 
transversions versus transitions. Then there are indels; do you want to take 
those into account?

Also, check the EMBOSS program 'msbar'.

You did not ask this, but... I remember that during the early days of Celera, 
one of the tools that enabled them to estimate the feasibility of the whole 
genome shotgun sequence assembly, was a very complete program to 'synthesize' 
in-silico the whole complexity of the human genome. I have no idea of that 
program is generally available now.

Yours,

    -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
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  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
___ _/_/_/_/_/________________________________________________________


More information about the Bioperl-l mailing list