I Need Help Analyzing This Graph From My Bioinformatics Textbook?

Question

[Adel]

It references a paper called "Highly Accurate Classification of Watson-Crick Base pairs on Termini of Single DNA Molecules" (by Winters-Hilt, Vercoutere, et. al)

I'm perplexed by the left side with A,B,C,D,E... - how does it relate the to the FSA on the right?

full image: http://i.imgur.com/cgwD6.png

Answer 1

[Laurakat]

The figure on the left is the sequence as it passes through a nano-pore. As each base proceeds through the pore it is held in place for a brief moment during which there is a change in ion current through the pore. In fact the change in ion current differs for each of the bases and thus you can read the sequence of the DNA as it moves through the pore. See http://en.wikipedia.org/wiki/Nanopore_sequencing for more information. The x-axis is therefore time as the DNA moves through the nano-pore and the y-axis is the conductance of the pore at that time. If you look at the original paper (free through PubMed Central) you can see how the pA values change for each base.

The figure on the right is a diagram of the base calling algorithm. It uses Hidden Markov Model and Support Vector Machines to analyze each base produced in the figure on the left. If you look at label E in the right figure it shows that you reset the model, while A starts the model. This is because you have switched to a new base. The rest of the parameters are to help filter noise/signal. Once you have hit the "sweet spot", if you will, (positions B,C,H,I, and L) you acquire the base. Put another way, the model is confident, given those values, that it knows what the base label should be.

You really should look at the full paper, it is a really cool system!

Answer 2

[Gjain]

the left side ABCDE are the states the DNA molecules and the right side shows the FSA of the transition between those states.

[Casey Bergman]

This can't be true since the x-axis of the graph is in units of msec, which means that the plot (and likely also the FSA) do not correspond to DNA at all. Probably the reference to [29] is a mistake.

[Gjain]

thanks for the clarification ... i saw the units but did not clarify it correctly ...