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Add some notes and URLs on ambiguous amino acids

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1 parent c779e72 commit 3539b7c557f2f3ba86bede48e363b9b9c115b0e6 @peterjc peterjc committed Mar 15, 2012
Showing with 16 additions and 1 deletion.
  1. +16 −1 Bio/Data/IUPACData.py
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@@ -5,9 +5,24 @@
# B = "Asx"; aspartic acid or asparagine (D or N)
# X = "Xxx"; unknown or 'other' amino acid
# Z = "Glx"; glutamic acid or glutamine (E or Q)
-# J = "Xle"; leucine or isoleucine (L or I, used in mass-spec)
+# http://www.chem.qmul.ac.uk/iupac/AminoAcid/A2021.html#AA212
+#
+# J = "Xle"; leucine or isoleucine (L or I, used in NMR)
+# Mentioned in http://www.chem.qmul.ac.uk/iubmb/newsletter/1999/item3.html
+# Also the International Nucleotide Sequence Database Collaboration (INSDC)
+# (i.e. GenBank, EMBL, DDBJ) adopted this in 2006
+# http://www.ddbj.nig.ac.jp/insdc/icm2006-e.html
+#
+# Xle (J); Leucine or Isoleucine
+# The residue abbreviations, Xle (the three-letter abbreviation) and J
+# (the one-letter abbreviation) are reserved for the case that cannot
+# experimentally distinguish leucine from isoleucine.
+#
# U = "Sec"; selenocysteine
+# http://www.chem.qmul.ac.uk/iubmb/newsletter/1999/item3.html
+#
# O = "Pyl"; pyrrolysine
+# http://www.chem.qmul.ac.uk/iubmb/newsletter/2009.html#item35
ambiguous_dna_letters = "GATCRYWSMKHBVDN"
unambiguous_dna_letters = "GATC"
ambiguous_rna_letters = "GAUCRYWSMKHBVDN"

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