[Bioperl-l] Transition-transversion hash in the evolve function - Bio::SeqUtils

[Mohamed Amine REMITA]

Hello,

The *%changes* hash in the *evolve()* function of *Bio::SeqUtils* module
would be like

$changes{'a'} = ['g', 'c', 't'];
$changes{'t'} = ['c', 'a', 'g'];
$changes{'c'} = ['t', 'g', 'a'];
$changes{'g'} = ['a', 't', 'c'];

rather than

$changes{'a'} = ['t', 'c', 'g'];
$changes{'t'} = ['a', 'c', 'g'];
$changes{'c'} = ['g', 'a', 't'];
$changes{'g'} = ['c', 'a', 't'];

if the first items of the arrays are for transitions.

Transition : Purine ↔ Purine or Pyrimidine ↔ Pyrimidine
Transversion : Purine ↔ Pyrimidine
http://en.wikipedia.org/wiki/Transition_(genetics)


The same thing for the function *_init_mutation_engine()* in*
 Bio::SeqEvolution::DNAPoint* module.

Thanks.

-- 
>Mohamed Amine Remita
Laboratoire de bioinformatique
Département d'informatique
Université du Québec À Montréal
514 987 3000 ext. 5576