Bioinformatics Computing

CSE 40532/60532 - Fall 2008

Instructor

Scott Emrich
Office: 351 Fitzpatrick Hall
Phone: (574)631-0353; E-mail: semrich at nd.edu
Office hours: Mon 11am-noon and 4:30-6:00 PM; Wed 4:30-6:00 PM; and by appointment

Teaching Assistant

Santanu Chatterjee
Office: 325 Cushing Hall
Phone: (574)631-3906; E-mail: schatter at nd.edu
Office hours: Tues 3:30-5:30 pm

Overview

Broad overview of bioinformatics with a substantial problem-solving component. Topics include: generative models for sequences, pairwise sequence alignment, basic methods in molecular phylogeny and evolution, ab initio gene prediction, whole genome comparisons, genome assembly and analysis.

Text and syllabus

Introduction to Computational Genomics by Cristianini and Hahn.

The syllabus can be found here

Announcements

Data for MEME run in homework #7
Small dataset and large dataset for Hw #6
Maize AMOS data Maize ref and bacteria AMOS data bacteria ref for Hw 5
Final project documentation now available
File 1 for Hw 2; File 2 for Hw 2
Please read Chapters 5 and 6 of the text.
File 1 and File 2 for Hw 3

Course material wiki

https://twiki.cse.nd.edu/twiki2/bin/view/CSE40532/WebHome

Schedule

Date	Topic	Homework	Notes
08/26/2008	DNA, genes and the genome		PDF
08/28/2008	Sequence statistics	HW #1 out	PDF
09/02/2008	Sequence alignment		PDF
09/04/2008	Sequence alignment		PDF
09/09/2008	Sequence alignment	HW #1 answers HW #2 out	PDF
09/11/2008	Sequence alignment		PDF
09/16/2008	Hidden Markov Models		PDF
09/18/2008	Hidden Markov Models		PDF
09/23/2008	Hidden Markov Models	HW #2 answers HW #3 out	PDF
09/25/2008	Ab initio gene finding		PDF
09/30/2008	Variation		PDF
10/02/2008	Variation and natural selection		PDF
10/07/2008	In-class midterm	HW #3 due
10/09/2008	Whole genome comparisons		PDF Add info
10/14/2008	Whole genome comparisons		PDF
10/16/2008	Whole genome comparisons		PDF Add info
Midterm Break!
10/28/2008	Genome sequencing and assembly	HW #4 out	Video 1 Video 2
10/30/2008	Genome sequencing and assembly		PDF
11/04/2008	Assembly validation	HW #4 due	PDF
11/06/2008	Intro to phylogentic analysis	HW #5 out	PDF
11/11/2008	Phylogenetic analysis		>PDF
11/13/2008	Phylogenetic analysis	HW #5 due HW #6 out	PDF
11/18/2008	Genome annotation		PDF
11/20/2008	Next-gen sequencing		PDF
11/25/2008	Motifs	HW #6 due HW #7 out	PDF
Happy Thanksgiving!
12/02/2008	Genomics in the news
12/04/2008	Special topics	HW #7 due
12/09/2008	Special topics
12/11/2008	Project presentations	Project due

Academic dishonesty

All are required to abide by the CSE and University honor code. Discussions are encouraged, but all answers/programs must be written/developed individually. Final projects will be performed as a group.