Week 5
Topics for this week:
How to find good anchors: suffix
trees
Their description, and an easy
quadratic-time algorithm
The big idea for this week of the course:
Suffix trees can do many
string operations you
might think are very
hard, in linear tim
Week 3B
Topics for this lecture:
Local alignment algorithms
Heuristic methods to make alignment
better
Two big ideas for this lecture:
Local alignments must be
computed heuristically to
avoid hideous runtimes.
There is some pretty great
computer science
Week 6
Topics for this week:
Beginning of sequence annotation
HMMs
Big ideas for the week
Models for sequences
let us identify their
important features.
Simple memoryless
models offer an ease in
specifying properties of
interest
CS 482/682, Fall 2014,
Week 4
Topics for this week:
Doing global alignment in linear space
Heuristic global alignment
Different anchor finding techniques
The big ideas of this week:
Global alignment
heuristics work via
forcing certain sites to
be matched in an
alignment
Ther
Week 2
Topics for this week:
Sequence alignment
Global alignment with affine penalties
Probabilistic models for evolution
A connection between the models and
optimal alignments
The big idea for this week:
The Optimal alignment
corresponds to the most
l
Week 3
Topics for this lecture:
Bayesian approaches to picking the
right model to give 2 sequences
Frequentist approach to assigning
alignment significance.
The big idea for this lecture:
The significance of an
alignment is how
probable it would be in
r
CS 482/682 Spring 2014
Assignment 2
Due at beginning of midterm, July 2
This is the second assignment for this course. As always, contact me or the TA if you have
trouble, and start as early as possible.
This assignment is worth 10% of your mark in the co
CS 482/682 Spring 2014
Assignment 1
Due at beginning of lecture, 28 May
This is the rst assignment for this course. As always, you should contact course staff if you
have trouble, and start as early as possible.
This assignment is worth 10% of your mark i