[Biopython-dev] [Bug 2548] New: Updating IUPACData and ExtendedIUPACProtein for U and O

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2548

           Summary: Updating IUPACData and ExtendedIUPACProtein for U and O
           Product: Biopython
           Version: 1.47
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


The IUPAC data in Biopython has not been updated to officially use X for any
amino acid and U for selenocysteine (Sec).  Nor do we support O for pyrrolysine
(Pyl) .

I haven't found an official statement from the IUPAC-IUBMB Joint Commission on
Biochemical Nomenclature via Google, but several major resources confirm this:

http://www.ebi.ac.uk/RESID/faq.html
http://www.uniprot.org/news/2008/02/26/release
http://doc.bioperl.org/bioperl-live/Bio/Tools/IUPAC.html

Patch to follow.


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