[Bioperl-l] Newbie Question

Hilmar Lapp hilmarl@yahoo.com
Sun, 25 Feb 2001 16:03:19 -0800

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