[BioPython] codons and complements

[Andrew Dalke]

Jeff Chang <jchang@SMI.Stanford.EDU>:
>NCBI has a reference for IUPAC amino acid definitions:
>http://www.ncbi.nlm.nih.gov/collab/FT/aa_abbrevs.html

This is the same as the IUPAC reference, as far as I can tell.

>NCBI has a FASTA format description, where they use '-' for gaps,

I've got no problem having the biopython standard for gaps being
'-' (note, this could be translated to "." or " " for the outside
world; I'm talking about an internal standard.)

>'U' for selenocysteine

Hmm.  IUPAC says
| U and O were avoided because U is easily confused with V in
| handwritten material, and O with G, Q, C and D in imperfect
| computer print-outs, and also with zero. J was avoided because
| it is absent from several languages.

I can see having U as the biopython standard name for
selenocysteine.  I would rather, however, use IUPAC definitions
as the internal form, but easily (dare I say "transparently" :)
support different alphabets.


>'X' for any amino acid, and '*' for stop codons:

Fine with me, though ditto on the alphabet pedandtry.  I don't
expect there will be any problem in the actual use of what I
proposed.  All it really does is hide better bookkeepping.

>The peptabiol database has a vocabulary for a bunch of
>non-standard amino acids (usually found in fungi):

>http://www.cryst.bbk.ac.uk/peptaibol
>http://sanda.cryst.bbk.ac.uk/peptaibol/nomenclature.html

Cool!  This is exactly what I wanted, since I knew there was
a need to support different alphabets for different uses, and
the mechanism I proposed is able to handle these.

>Using SEC and X for selenocysteine first used in;
>Gunzler WA, Steffens GJ, Grossmann A, Kim S-MA,
>Otting F, Wendel A, and Flohe L.  (1984)
>Hoppe-Seylers Z. Physiol. Chem.  365, 195-212.

The IUPAC reference I gave for protein sequences lists the
reference in the addendum.

						Andrew Dalke
						dalke@acm.org

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