I am doing an exam question, its looking for a position frequency matrix and then to sketch a sequence logo.
I understand the matrix but I am unsure about the calculations for logo. As far as I know their formula for sequence logo is incorrect and should be ''2 + ...'' instead of ''2 - ...''
So for the second column if I use the correct formula, I get G=1.58 C=1.5 A=1.625 and then I have to multiply each of these by their frequencies to get the actual information content heights. So G will now be 0.99 bits, C will be 0.375 and A will be 0.2
Therefore my logo in that column at the bottom will have a small A to the height of 0.2 bits, then a C to a height of 0.575 (0.375 + 0.2) and G to a height of 1.565 bits (0.99 + 0.375 + 0.2)
Am I correct with this?
I understand the matrix but I am unsure about the calculations for logo. As far as I know their formula for sequence logo is incorrect and should be ''2 + ...'' instead of ''2 - ...''
So for the second column if I use the correct formula, I get G=1.58 C=1.5 A=1.625 and then I have to multiply each of these by their frequencies to get the actual information content heights. So G will now be 0.99 bits, C will be 0.375 and A will be 0.2
Therefore my logo in that column at the bottom will have a small A to the height of 0.2 bits, then a C to a height of 0.575 (0.375 + 0.2) and G to a height of 1.565 bits (0.99 + 0.375 + 0.2)
Am I correct with this?
