SoniaT: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
No edit summary |
mNo edit summary |
||
Line 12: | Line 12: | ||
==Parsimony Continued== | ==Parsimony Continued== | ||
*Why parsimony? | |||
**that will become more clear later when we go over likelihood | |||
**this algorithm is sometimes called "model-free" because the model is implicit | |||
**we can suggest infinite alternative explanations involving increasing numbers of mutations but they become less and less plausible | |||
*One '''not'''-optimal way to look for the most parsimonious tree: try all four possibilities at every node. But that would require looking at 4^n possibilities! Using recursion in this problem, we can avoid that. | |||
=== Down-Pass Algorithm=== | === Down-Pass Algorithm=== | ||
*Formalizing the idea of what you did by intuition in HW1. | |||
<blockquote><tt> | <blockquote><tt> | ||
Line 26: | Line 34: | ||
</tt></blockquote> | </tt></blockquote> | ||
Line 38: | Line 41: | ||
*Consider different weights for different mutations: P(transitions > P(transversions) | *Consider different weights for different mutations: P(transitions > P(transversions) | ||
#Lets say that the cost of no mutation is zero, so fill in the diagonal | #Lets say that the cost of no mutation is zero, so fill in the diagonal with zeros. | ||
#Lets say we want the cost of a transversion to cost 2.5 times as much as a transversion | #Lets say we want the cost of a transversion to cost 2.5 times as much as a transversion | ||
#On the leaves we want to do something different from the internal nodes, because we are 100% sure of what the sequence is; it's not a guess. | #On the leaves we want to do something different from the internal nodes, because we are 100% sure of what the sequence is; it's not a guess. | ||
Line 45: | Line 48: | ||
#If we work down from leaves to root | #If we work down from leaves to root | ||
example tree: ((C,A),(C,(A,G)) |
Revision as of 08:31, 18 September 2006
I'm a second year student in Eric Alm's and Bruce Tidor's Labs.
This term (Fall06) I'm TA-ing the undergrad computational class 20.181.
Check out the new BE directory!
Temporary notes for 20.181, Lecture 4
Review of Homework #1
Parsimony Continued
- Why parsimony?
- that will become more clear later when we go over likelihood
- this algorithm is sometimes called "model-free" because the model is implicit
- we can suggest infinite alternative explanations involving increasing numbers of mutations but they become less and less plausible
- One not-optimal way to look for the most parsimonious tree: try all four possibilities at every node. But that would require looking at 4^n possibilities! Using recursion in this problem, we can avoid that.
Down-Pass Algorithm
- Formalizing the idea of what you did by intuition in HW1.
def downPass(tree): #pseudocode!
- if tree is a leaf:
- return seq
- l = downPass(left child)
- r = downPass(right child)
- i= l <intersect> r
- if i==None:
- return l <union> r
- return i
Sankoff Downpass Algorithm
- Consider different weights for different mutations: P(transitions > P(transversions)
- Lets say that the cost of no mutation is zero, so fill in the diagonal with zeros.
- Lets say we want the cost of a transversion to cost 2.5 times as much as a transversion
- On the leaves we want to do something different from the internal nodes, because we are 100% sure of what the sequence is; it's not a guess.
- Initialize tree; each leaf has a vector of length 4
- put a score of zero for the letter that we KNOW it is, put a score of infinite for the other three.
- If we work down from leaves to root
example tree: ((C,A),(C,(A,G))