pi_lec5

# pi_lec5 - 20.181 Lecture 5 Contents 1 Downpass (cont.) o...

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20.181 Lecture 5 Contents 1 Downpass (cont.) o 1.1 Sankoff Downpass Algorithm o 1.2 Downpass: can we stop there? 2 Fitch's upPass Downpass (cont.) The tree we were working on last time: Now we're going to try to code up the downpass. 1. So now we want to know: what is the sequence at this ancestor node, that we can't observe? We'll try all four possibilities, and calculate the penatly associated with each of those possibilities are. 2. Remember that the good solution with the fibonacci series was to pass all the information back each time so that we don't have to repeat calculations! 3. We left off at the root node, where we said there were 64 possibilities. 4. So let's go through this by hand and try to write pseudo code for a function that will do the same thing.

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5. What we're going to do, which might seem odd at first, is to pass the node's identity (nodeSeq) (A,C,G,or T) into the function as if we know it. Our function will look at this one possibility and return one column of the cost vector. We will
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## This note was uploaded on 11/11/2011 for the course BIO 20.010j taught by Professor Lindagriffith during the Spring '06 term at MIT.

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pi_lec5 - 20.181 Lecture 5 Contents 1 Downpass (cont.) o...

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