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

[Aaron J Mackey]

On Thu, 13 Jul 2000, Heikki Lehvaslaiho 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. 

Synonymous and nonsynonymous usually refer to codon mutations, i.e. a
mutation which continues to encode the same amino acid (due to genetic
code redundancy) is a synonymous mutation.  Nonsynonymous mutations affect
a change in the encoded amino acid.  It's not in the sense of "isoleucine
is synonymous to leucine" - that's a scoring-matrix derived comparison.

-Aaron

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