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

Heikki Lehvaslaiho heikki@ebi.ac.uk
Wed, 10 Jan 2001 12:26:53 +0000

I noticed that it is not possible to use three letter codes for amino
acids in any bioperl sequence objects. I think should be possible at
least to output in three letter code. Mapping three letter code back
to one letter code is not too hard, either, but is it a good idea to

I propose to put method 'seq3' into PrimarySeq.pm which is called from
Seq.pm, too.

=head2 seq3

 Title   : seq3
 Usage   : $string = $obj->seq3()
 Function: Read only method that returns the amino acid sequence 
           as a string of three letter codes. moltype has to be 
           'protein'. Output follows the IUPAC standard plus 
           'Ter' for terminator.
 Returns : A scalar
 Args    : character used for stop, optional, defaults to '*'
           character used for unknown, optional, defaults to 'X'


Any opinions?


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     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
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