[Bioperl-l] three letter codes for amino acids?

[Heikki Lehvaslaiho]

> Considering sequence atoms as symbols seems the most natural
> concept to me. Having single letters representing each symbol
> makes symbol arrays and strings more or less equivalent in Perl.
> This might not hold for multi-letter representations, so in the
> first place I'd expect an array to be returned. However, this is
> inconsistent with $seq->seq(), and reportedly inefficient due to
> Perl's array implementation.
> 
> I know you could still split at every 3rd letter as a simple way
> to get an array. I'd nevertheless accept a third optional
> parameter denoting the 'join' character, with a default of ''.

Can be done.

In my mind the main use of this function is in displaying translations
on top of nucleotide sequnces. Gaps inside codons are clearer with
the three letter coding.

	-Heikki


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