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4.0 years ago
2001linana
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40
Hi. I read something like " Only 11 sites show polymorphism in >5% of sequences; yet two mutations, including the D64G mutation in Spike, have already become consensus." I was wondering, what is the meaning of "consensus mutation" then? Many thanks for your time and attention.
I believe when we perform a multiple sequence alignment, for each position the most frequent nucleotide can be called "consensus". So in this situation I guess more than half of the samples have this mutation.
You mean the most frequent nucleotide is called "consensus".
Not necessarily. Sometimes we have positions where the different muations frequencies are not very infromative. Eg. A has a freqiency of 30%, c 25%, g 25%, t 20%. Instead of calling A a consensus, we put N in the consensus sequence.
So, it is only called "consensus" if the frequency of this mutation site is more than 50%, as you have mentioned earlier.
As for everything in bioinformatics, there is no strict consensus on it...
I see, because it is a vague subject.
Moreover, some computational logics in bioinformatic articles are lacking...
I absolutely agree with you, even though I am a part of this problem
haha... Hope we can discuss / cooperate more in the future about various topics. I'm mainly in the computational side currently.
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