BME 230: Computational Genomics

Spring Quarter, 2004

 

* Homeworks *

* Student Genome Browsers *

* Course Links *

* Reading List *

   

Time:

TuTh 2-3:45pm

Location:

Baskin Engineering, Rm 372

Course Link:   

http://www.soe.ucsc.edu/classes/bme230/Spring04/    

 

Instructors

Todd Lowe

Josh Stuart   

Email

lowe@ soe.ucsc.edu  

jstuart@ soe.ucsc.edu    

Office

227 Sinsheimer Labs

129 Baskin Eng

Office Hours

Wed, Thur 4-5pm
    & by appt.

Mon 11-12

Wed 2-3

 

Textbooks

Biological Sequence Analysis by Durbin, Eddy, Krogh, & Mitchison

Bioinformatics: Sequence and Genome Analysis by David Mount

Grading

90%

Homework / Problem sets

 

 

10%

Final exam (take-home)

Syllabus

Date

Lecturer

Lecture

Topics

Reading

Assignments

March  30

Stuart
Lowe

Course Overview
Introduction: Genomes

Historical Perspective
Genome Sequencing

Mount, Ch 1, 2 (pp 20-29)

 

April 1

Stuart


Pairwise Sequence Alignment

Dot Plots
Dynamic Programming
Global v. Local
Scoring Matrices

Durbin, 2.1-2.4
Mount, Ch 3 (pp 51-96)

HW1:
Getting to Know
Your Genome

April 6

Kent




The 'Kent' Code Base     

The browser staff 
CVS access to the code
Object oriented programming in C
Code conventions
Strings, hashes etc
Databases & Code Generators
Biological Analysis Stuff

 

 

April 8

Lowe



BLAST

FASTA
BLAST Family of Programs
BLAST Statistics
Significance of alignments
EVD's
Tweaking Searches

Durbin, 2.5-2.9
Mount, Ch 3 (pp. 96-137),
Ch 7 (pp. 291-314)

HW2:
Pairwise alignment,
Adding your first Browser
tracks

April 13

Stuart


Multiple Sequence Alignment 

Aligning more than 2 sequences
Finding regulatory motifs in unaligned sequences
Gibbs sampling

 

 

April 15

Haussler

HMMs

(Special thanks to Bernard Suh for scribing)

Principles of HMMs

HMMs for gene finding

Durbin 3.

 

April 20

Haussler

 

HMMs

(Special thanks to Bernard Suh for scribing)

Viterbi algorithm for most likely hidden state path

Forward & backward algorithm for probability of a sequence

Higher-order markov chains

 

 

April 22

Kent


Advanced Pairwise Alignment
and Assembly

(Special thanks to Bernard Suh for scribing)

Heuristics for finding homologous regions
Chaining local alignments
Genome mapping
Genome assembly

 

 

April 27

Stuart

 

HMM learning

HMMs for pairwise & multiple sequence alignment

Learning HMM parameters from observations

Expectation-Maximization with Baum-Welch

Durbin 4-6

 

April 29

Lowe

 

RNA Genomics

RNA structure and function
Specialized RNA Genefinders

QRNA, MFOLD


Eddy, Nature Reviews

RFAM paper

HW3: HMMs


May 4


Stuart


Heuristic

Phylogenetic reconstruction

Trees

Distance Methods: UPGMA, Neighbor-joining

Parsimony

Bootstrapping

Durbin, Ch 7
Mount, Ch 6

 

 

May 6

Stuart

 

 

Probabilistic Phylogenetic reconstruction

Likelihood
Stationary markov processes

Rate matrices

Maximum Likelihood

Felsenstein’s Post-order traversal

Bootstrap revisited

Maximum a posteriori

Sampling posteriors

Durbin Ch. 8

HW4: Fun with ncRNAs



May 11

Lowe


RNA Genomics (cont) & Grammars


 

 

 

Durbin Ch. 9-10
Mount, Ch 5

 

 

 

May 13

Lowe

 


Stuart

 

RNA Folding


Probabilistic Phylogenetic reconstruction (cont)

Minimum free energy structures
Mathews structure prediction using DynAlign

 

 

 


Durbin Ch 8


 

 

May 18

Siepel

Evolutionary reconstruction

Part I (Cold Spring Harbor Talk)

 

Part II

PhyloHMMs

Siepel & Haussler 2004

 

May 20

Lowe


Genome Analysis: "Other" Genome Components

 

 


Comparative Genomics

Repeats (Repeat masker, RECON)
Transposons,
Structural features of genomes,
Pseudogenes

Distinguising orthologs from paralogs (gene trees)
COGs


Mount, pp. 487-495

 

 


Mount, pp. 500-524

 

Hmwk #5:
Phylogenetic reconstruction

May 25

Haussler

Whole-genome comparative genomics

 

 

 

May 28

Stuart

Joint-learning I

Probabilistic Graphical Models

Bayesian Networks

Conditional Independence

Dynamic Bayesian Networks generalize HMMs

 

 

N Friedman 2004.

 

June 1

Stuart


Joint-learning II

Inference in Bayesian Networks

Probabilistic relational models

Identifying cis-regulatory elements


E Segal et al 2003.

 

June 3

Stuart


Human Sequence Variation

SNPs
Haplotype inference
Pharmacogenomics