I am having trouble with this university exam question..
My understanding is that the elements within the PWMs above were calculated using the formula log2(frequency/0.25) and then had pseudocounts added.
I do not know what value of pseudocounts were used but by looking at the 3rd column of PWMx there are three -4.5 values so these may have had frequencies of 0 while the C had a frequency of 1 and when pseudocounts were added to it, it became 3.9.
If I know the original frequencies of the bases, I can use the formula; 2 + fbi x log2(fbi) and then multiply by fbi again to find the information content. However I do not know the frequencies by looking at these values.
My guess is that minus values would have a very small information content while large plus values would have a high information content thus if you have lots of low (minus) values and lots of high (plus) values, you will yield a higher information content.
Also as PWMx consists of 6 binding sites and PWMy only has 4 binding sites, would PWMx naturally have a higher information content as it has more binding sites?
Just to be clear: Is this a question you are being evaluated with?
Yes, this type of question may come up in my exam in 3 weeks.
So it NOT your actual exam, it's a question from previous exams, is that correct?
Correct. I am thus practicing how to do previous questions as they may come up again.
That is great but please show some effort and specify where you have a gap, it will be easier to help you this way. Don't expect people to give you the whole introduction to information theory here.
Yes, sorry. I should have been more specific in what is troubling me about the question. I have now edited the question including my interpretation of it.
If this is not your homework or the exam, it should be a viable solution to do this the old-fashioned way: ask your instructor. I would be happy to help my students with their practice exams, but am hesitant to undermine other instructors by helping their students with something that looks like homework to me.
Hi Mensur, I tried doing what you suggested. I reached out to my instructor, however, I have been unable to get in contact with him. We are not in university at the moment either, for obvious reasons, therefore I have no way of getting help. Could you at least guide me in this question to get me on the right track? I have included my interpretation of the answer in the question. Many thanks