Coverage for Bio.Alphabet.IUPAC : 100%

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# Copyright 2000-2001 by Andrew Dalke. # Revisions copyright 2008 by Peter Cock. # All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package.
##################### Protein
# From the IUPAC definition at: # http://www.chem.qmw.ac.uk/iupac/AminoAcid/A2021.html#AA21
"""Extended uppercase IUPAC protein single letter alphabet including X etc.
In addition to the standard 20 single letter protein codes, this includes:
B = "Asx"; Aspartic acid (R) or Asparagine (N) X = "Xxx"; Unknown or 'other' amino acid Z = "Glx"; Glutamic acid (E) or Glutamine (Q) J = "Xle"; Leucine (L) or Isoleucine (I), used in mass-spec (NMR) U = "Sec"; Selenocysteine O = "Pyl"; Pyrrolysine
This alphabet is not intended to be used with X for Selenocysteine (an ad-hoc standard prior to the IUPAC adoption of U instead). """
"""Uppercase IUPAC protein single letter alphabet of the 20 standard amino acids."""
##################### DNA
# The next two are the IUPAC definitions, from: # http://www.chem.qmw.ac.uk/iubmb/misc/naseq.html """Uppercase IUPAC ambiguous DNA."""
"""Uppercase IUPAC unambiguous DNA (letters GATC only)."""
# Also from the URL, but not part of the standard """Extended IUPAC DNA alphabet.
In addition to the standard letter codes GATC, this includes:
B = 5-bromouridine D = 5,6-dihydrouridine S = thiouridine W = wyosine """
##################### RNA
"""Uppercase IUPAC ambiguous RNA."""
"""Uppercase IUPAC unambiguous RNA (letters GAUC only)."""
# are there extended forms? #class ExtendedIUPACRNA(Alphabet.RNAAlphabet): # letters = extended_rna_letters # # B == 5-bromouridine # # D == 5,6-dihydrouridine # # S == thiouridine # # W == wyosine |