[Bioperl-l] Bio::Tools::OddCodes

Will Fischer wfischer@indiana.edu
Thu, 13 Jul 2000 11:33:53 -0500

"synonymous" changes are mutations in the DNA sequence that don't
change the amino acid encoded (e.g. ttc -> ttt, both encoding Phe);
"non-synonomous" mutations do change the amino acid encoded 
(e.g. ttc -> tta, Phe -> Leu), and the mutant gene therefore
produces a different protein product.

So it's not a way of classifying amino acids at all...

-- Will
Will Fischer
Biology Department                      wfischer@indiana.edu
Indiana University                      Lab:   812-855-2549
Jordan Hall 142                         
1001 E. Third Street                    FAX:    812-855-6705
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On Thu, 13 Jul 2000, heikki@ebi.ac.uk wrote:
In a related note: I'd like to ask if anyone on the list might know is
there is commonly agreed definition to yet an other way of amino acid
change classification: Synonymous and non-synonymous are commonly used
terms in population genetic papers to classify coding region mutations
but they are never defined. Most probably their definiton is based on
something similar to Derek's 'functional' alphabet. 

Can anyone tell me if synonymous amino acid changes are _identical_ to
Derek's functional change?