[Bioperl-l] Tool to mutate DNA sequence

[Ryan Golhar]

Thanks all.  The responses I got were definitely more than helpful.  FYI
- I did initially look at msbar.  I glanced over the "Number of times to
perform mutation operations", which is what I was looking for.  

I'm looking to statistically test some simply scoring matrices.  I think
msbar will do.

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: Thursday, February 09, 2006 9:55 AM
To: bioperl-l at lists.open-bio.org; golharam at umdnj.edu
Cc: 'The general forum at Bioinformatics.Org'; 'bioperl-l';
emboss at emboss.open-bio.org
Subject: Re: [Bioperl-l] Tool to mutate DNA sequence


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
>
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> Bioperl-l at lists.open-bio.org 
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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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