I have an MSA of homologous sequences of beta-turn for which I have calculated the turn type (I'/II'/I/II). Now to quantify in terms of a score for the conservation of turn types, which statistical method can be used? I looked for Shannon sequence entropy scoring method which is commonly used in scoring MSA. Can that be used in my case?
Hey Bharat,
In addition to Shannon's sequence entropy (which I think is the first one you try because it's easiest to implement?), you have LOADS of cool conservation algorithms to play with.
One that might be of use to you is the rate4site algorithm from the Ben-Tal group. I particularly like this one because it also considers the evolutionary (phylogenetic) distance between the sequences that you're using. For example, if you have 20 orthologues in your MSA and 15 of them are extremely close in terms of distance then I don't think conservation values would mean as much compared to the scenario where the orthologues are really distant -> From the SE equation, I don't think you take such information into account which would be very useful I feel.
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