Talk:Ka/Ks ratio

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John Timmer (December 29, 2015). "Editorial: Wikipedia fails as an encyclopedia, to science's detriment". Ars Technica.

Synonymous sites

This article does not make it clear what is meant by a synonymous or non-synonymous site; the definitions of these also seem to be non-obvious (see http://pubmlst.org/software/analysis/start/manual/dsdn.shtml). — Preceding unsigned comment added by 24.213.110.213 (talk) 19:35, 16 December 2012 (UTC)[reply]

I came to the talk page to make exactly the same point (ask the same question). i.e. what is a synonymous vs. a non-synonymous site? By site I take it to mean a column of a multiple sequence alignment, but how is a site synonymous or not? --Dan Bolser (talk) 22:10, 9 November 2014 (UTC)[reply]

Further to the Ars Technica article mentioned in the header above, I came to this article to see if its readability could be improved for general readers. However, despite being a biologist (trained last century, admittedly), I came unstuck on this same issue that the two previous commentators did. I understand what synonymous means in the context of base changes (and that'd be easy to articulate for a general reader), but I can't work out what a synonymous site is. It's not helped by the fact that there's no linked article, nor are the articles that are linked helpful on this point. Can anyone advise? --PLUMBAGO 09:37, 6 January 2016 (UTC)[reply]

Me too. I'm pretty used to improving biology articles, and am similarly qualified to User:Plumbago, but John Timmer had a point in his Ars Technica article about this particular Wiki-specimen. It's a bit embarrassing to have Signpost (6 Jan 2016) pointing to bad science writing here, so perhaps we can work out what this article was trying to say, and do it a little less "impenetrably". At the moment, it's frankly at mermaid level. Chiswick Chap (talk) 12:59, 16 January 2016 (UTC)[reply]

In case it helps, the number of synonymous "sites" is calculated as the number of possible changes in a base that would be synonymous. Any base can change to any of the three other bases. A codon (three bases) can thus change to 9 possible codons (any one change in one of the three bases). The number of synonymous sites was originally calculated as the number of possible codon changes that are synonymous (same for non-synonymous sites). This is the simplest model assuming that all of the 9 base changes are equally likely (Nei & Gojobori's version of dN/dS, 1986). However, since not all base changes are equally possible, more advanced maximum-likelihood methods take the different mutability of each base into account in calculated the relative neutral probability of synonymous and non-synonymous changes. 185.118.205.91 (talk) 08:47, 11 May 2018 (UTC)[reply]