[BioPython] codons and complements

[Andrew Dalke]

Iddo Friedberg <idoerg@cc.huji.ac.il>:
>Does the IUPAC alphabet take care of stop codons seperately? We
>need to differentiate between an unknown/irregular aa in the
>sequence, and a stop sign, which, as you pointed out, should be
>signified & user-treatable.

No.  IUPAC doesn't define a 1- or 3- letter code for stop
codons.  They propose "X" for selenocysteines, and have
recommendations for gap characters ("-", "." and " "), but that's
it.

The IUPAC definitions are at:
  http://www.chem.qmw.ac.uk/iupac/
but I can't seem to refind the recommendations for gap characters.

						Andrew

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