Can anybody tell me what is the meaning of the numbers in the attached picture?
The picture is the upstream of a promoter.
If those values are conservation values, it means that the given percentage of sequences analyzed (subscript) had the nucleotide shown in that position.
The figure shows a consensus sequence obtained from the alignment of an n number of sequences (n=100% and all the subscript values are relative to n). The bigger the number, the more conserved a site is; on the other hand, the lower the value, the bigger the variability observed at that given site in the alignment.
Please note that a lower conservation shows a bigger OBSERVED variability on the sample, i.e., it depends on how representative are your sequences. If, and only if, the sequences aligned correspond to a representative sample of your whole set of sequences/organisms then you can make an inverse correlation with the mutation rate. That would be as you stated it: the lower the value, the bigger the chance of a mutation on that given site. This will only be true if your sample is big enough or if you are sure that the chosen sample is a representative one.
It gives the position between the ATG start on ORF (e.g,TATA BOX at -10).. ATG is considered +1
I agree with Swaminathan, it is most likely to be the conservation of that nucleotide in that particular postition of the alignment. It's a notation I have never seen before, though.
The value Slimane is refering to is the big number at the top of the image, which does represent the position of the consesus sequences shown in the figure.
Thx all! I also agree with Swaminathan. It is rare to mark like this.
So does it means smaller the number, bigger the chance to mutate?
If those values are conservation values, it means that the given percentage of sequences analyzed (subscript) had the nucleotide shown in that position.
The figure shows a consensus sequence obtained from the alignment of an n number of sequences (n=100% and all the subscript values are relative to n). The bigger the number, the more conserved a site is; on the other hand, the lower the value, the bigger the variability observed at that given site in the alignment.
Please note that a lower conservation shows a bigger OBSERVED variability on the sample, i.e., it depends on how representative are your sequences. If, and only if, the sequences aligned correspond to a representative sample of your whole set of sequences/organisms then you can make an inverse correlation with the mutation rate. That would be as you stated it: the lower the value, the bigger the chance of a mutation on that given site. This will only be true if your sample is big enough or if you are sure that the chosen sample is a representative one.
___Upstream______________+1__________down stream__________
+1: transcription start point
For example, -35 means 35 nts to the left of the transcription start point ( the location of the start codon)
Hi, Kamel. Now I see what you are talking about. Yes, I agree with your opinion.
Actually, I am asking about the subscript number in the bottom-right cornorn of every nucleotide. i.e. T85. talking about the number 85. According to Swaminathan and Slimane, it seems to represent the conservation of that nucleotide.
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