[Bioperl-l] Method dnaseq in EncodedSeq not working properly?

[Steffen Grossmann]

Dear all,

am I wrong or does the method "dnaseq" of Bio::Seq::EncodedSeq not do 
what is promised in the documentation? I understand the documentation 
such that e.g. with the command

@introns = $obj->$dnaseq(-encoding => 'I')

I would get a list of all the parts in the sequence which are coded with 
an 'I'. (From a look at the method's code I'd say it doesn't do anything 
at all...)

Actually, what I really need is a way to identify pieces of repeated X's 
or N's from DNA sequences in order to exclude them from a sequence-wide 
screening for good hits of a position-weight-matrix. Any hint concerning 
that problem is highly appreciated! Since I am a bioperl-newbie maybe I 
only suffer from a lack of overview...

Steffen
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%            Steffen Grossmann                %
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