Talk:Substitution matrix

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A stab by someone who's more a student of the topic than an expert on it =)

Please feel very very free to make any changes you want.

Well, what is the i-j entry of the matrix? At least you should write down the definition! -wshun 06:29, 11 Nov 2003 (UTC)

Good point. I've now included a definition of log-odds scores.

Reorganisation of Molecular Evolution

I noticed several overlaps and missing aspects in these molecular evolution articles:

Substitution model

Substitution matrix

Models of DNA evolution

Models of protein evolution

When there are no objections, I will reorganize, partly rewrite and extend these articles in the next few days. I would welcome any advice, especially on other related articles that I am not yet aware of.

My concept looks as follows:

Substitution model as the main article will discuss the mathematical background. Here I will explain also the Markovian model of evolution which is common to most models and is the basis of several aspects already mentioned on this page. The description of the DNA models will be moved to Models of DNA evolution and only briefly be summarized in the general article. The Models of protein evolution will also be summarized and explained in all detail in the new Models of protein evolution article.

The Substitution matrix article should focus on the log-odds matrices and their applications, mostly for dynamic programming/alignments. The description of the different matrices needs to be extended (JTT, Gonnet and GTR at least) and will be moved to the new Models of protein evolution article.

09:13, 5 October 2006 (UTC)

Thanks for your note. Well, your idea is logically sound, but I think most people (at least the biology-bioinformatics crowd I hang out with) don't like too many subdivisions, my original idea when I made those stubs was to have both the Markov models and the particular DNA models in one article. I agree that there will be duplication with the article on Substitution models, but there are ways to manage duplication (for example, one could be more mathematically detailed and the other more perspective based). Why don't we do the following: give me until this Sunday. I will write my version of the models of DNA evolution article, in the way that I originally envisaged it. We can then compare notes and decide the next step in terms of reorganization etc. Will that be OK? Sanjay Tiwari 11:58, 5 October 2006 (UTC)

PS And I mean the same for the article Models of protein evolution. When I created the template for Topics in molecular evolution, I had a certain approach to models of protein evolution in mind. I will attend to that early next week. Once that is in place, we can discuss it, how to amend it. Will that too be OK? At the worst, what I will write will be thrown out in its entirety, but that will be fine. Sanjay Tiwari 12:07, 5 October 2006 (UTC)

Thank you for your comment. I also prefer comprehensive, longer articles. My concern was that having Markov models and DNA models and protein models all in one article might be too much. But your suggestion sounds reasonable. So I'm looking forward to see your version early next week. Then we can discuss the details. wild8oar 07:06, 6 October 2006 (UTC)

Thanks for your comments and for your original note above. It got me off my butt and working! Otherwise, it might have lain unattended for who knows how long. Talk to you next week. Sanjay Tiwari 20:58, 6 October 2006 (UTC)