Syllabus for CMSC423: Bioinformatic Algorithms, Databases, and Tools (Fall 2009)

Course information

GLUE HOWTO

Bioinformatics seminars

CS Grade Server (grades.cs.umd.edu)

Tentative syllabus

Date

Topics

Slides/Lecture notes

Add'l resources

09/01

Introduction

Lecture 1 - Intro & policies


09/03

Molecular biology primer

Bio-Introduction
Homework 1 (PDF, ODF, DOC)
Book: Chapter 1


09/08

Molecular biology primer - PCR, sequencing

Programming for Bioinformatics

Homework 1 due

Bio-Programming, utilities
Book: Chapter 1
Book: Appendix A

www.bioperl.org
www.biojava.org
www.biopython.org
www.bioruby.org
www.bioconductor.org

09/10

Bioinformatics Databases

Homework 2 (Project part 1)

Bio - Databases
Book: Appendix B


09/15

Sequence alignment - exact matching

Exact matching: basics

Admin notes
no book chapter

Dan Gusfield's book

09/17

Sequence alignment - exact matching

Homework 2 due

Lecture 6
no book chapter

KMP algorithm:
http://www.inf.fh-flensburg.de/lang/algorithmen/pattern/kmpen.htm

http://www.ics.uci.edu/~goodrich/dsa/11strings/demos/pattern/

http://www-igm.univ-mlv.fr/~lecroq/string/

http://www.cs.ubc.ca/labs/beta/Courses/CPSC445-08/Handouts/kmp.pdf

09/22

Suffix trees

Admin notes

Exact matching: suffix trees
no book chapter
Homework 3 (PDF, ODT, DOC)

Bowtie paper

zvalues.c - software to compute zvalues

09/24

Suffix arrays

Data compression

Lecture 8


09/29

Suffix trees/arrays & midterm recap


Homework 3 due

Homework 3 solution

10/01

Midterm 1

basic biology + exact matching

Sample midterm

10/06

Sequence alignment - inexact matching

Inexact alignment
Chap.6

Dr. Pop out of town


10/08

Midterm recap

Alignment heuristics

Chap. 6

Project Part 2 handed out

10/13

Sequence alignment - inexact matching


Admin

10/15

Sequence alignment - inexact matching, affine gaps



10/20

Sequence alignment heuristics

Chaining algorithms

Alignment heuristics

Project part 2 due

Admin

10/22

Multiple sequence alignment

Motif finding

Multiple sequence alignment

Chap. 6.7

ClustalW
Muscle
Gibbs sampling

10/27

Genome sequence assembly

Genome assembly
Chap. 4.5
Chap. 8

Assembly primer

10/29

Genome sequence assembly



11/03

Phylogenetic trees

Tree analysis/display

Phylogenetic trees

Chapter 12

Project part 3 due


11/05

Midterm 2



11/10

Phylogenetic analysis



11/12

Genetic association studies

Genetics

Chap. 13


11/17

Genetic association studies



11/19

"Signal" finding
Gene finding

Hidden Markov Models

Gene finding

not in book


11/24

Data clustering

Data clustering

Chap. 11.1-11.6
Chap. 10


11/26

Thanksgiving

no class


12/01

RNA structure prediction

RNA structure prediction

not in book


12/03

What you missed...
proteomics
protein structure prediction
gene networks
association studies

What you missed

Final project due!!!


12/08

Recap
What to expect at a job interview



12/10

Recap/Review



12/14

Final exam

CSIC 1121, 8-10am