HMM
Chapter 3 of the textbook
1
Sunday, October 24, 2010
Outline
CpG island
Markov chain
Hidden Markov model
2
Sunday, October 24, 2010
CG suppression
This is a sequence from human genome
GCCTACACACCGCCAGTTGTGTTCCTGCTATGTCTCTAGTGATCCCTGAA
AAGTTCCAGCGT

Introduction
CS482/682
1
Outline
Course logistics
A few example problems
CS 482/682 Fall 2007 Week 1
2
Course staff
Instructor: Bin Ma (DC 3345, binma@uwaterloo.ca,
http:/www.cs.uwaterloo.ca/~binma)
TA: Lian Yang
Course webpage:
http:/www.cs.uwaterloo.ca/

Multiple Alignment
1
Things to Study
Model
Insert gaps to sequences so that letters in
each column are similar.
Scoring function
relative entropy
SP score
Algorithm
Exact algorithm
Heuristic algorithm
Approximation algorithm
Applications
2
From

Motif Finding
1
Outline
Motif
Motif Evaluation (scoring function)
Heuristic Algorithm
Other Models of Motif Finding
Closest substring, Consensus pattern.
A Fixed Parameter Algorithm for Closest
String.
2
Motif
In genetics, a sequence motif is a
nucleot

Seeding Methods in Homology Search
1
Heuristic algorithms
Heuristic algorithms are basically
algorithms for the real world.
They acknowledge that the real world is
complicated, and you cant always get
what you want.
A heuristic algorithm promises to
pr

Alignment Score and Alignment
Signicance
1
Optimization Problem
Instance: describes the input
Feasible Solution: describes the format of the
output
Score Function: measures how good a solution is
Objective: either maximize or minimize the
score.
For S

Sequence Alignment
1
Overview
Edit distance
Alignment
Arbitrary gap penalty function
2
Sequence is cheap, everything else is expensive
Its pretty cheap to sequence DNA at this
point; hundreds of genomes have been
sequenced, and another thousand or so
a

More Alignments
1
Outline
We have learned
The basic DP algorithm for alignment
The general gap penalty
The affined gap penalty
Now let us study several other models of
alignments
Local alignment (to compare substrings)
Fit alignment (to embed one s