[Bioperl-l] Newbie Question

[Hilmar Lapp]

"Schreiber, Mark" wrote:
> 
> Hi,
> 
> How does bioperl cope with DNA sequences containing N's? Particularly I am
> interested in the behaiviour of the Sequence and SeqIO modules.
> 

In general there is no difference between sequences with and
without ambiguity symbols. The translation code tries to translate
what it can translate (i.e., even if there's an ambiguity symbol
in a codon, but the amino acid is unambiguously determined, you
won't get an X). For nucleotide sequences with an excessive number
of degenerate bases you might need to specify -moltype => 'dna' at
instantiation, because the type-guess code might be confused, but
I'm not sure.

The SeqIO modules are not affected at all, except for the last
point I mentioned (they don't set -moltype).

Does that answer your question?

	Hilmar
-- 
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Hilmar Lapp                              email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
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