BNFO 601: Foundations of Bioinformatics I
Fall 2008

Instructor: Usman Roshan
Office: GITC 3802
Ph: 973-596-2872
Office hours: Monday 2:30-4pm and Thursday 11:30-2pm
Email: usman@cs.njit.edu

Recommended Textbooks:

• An Introduction to Bioinformatics Algorithms by Pavel Pevzner
• Biological Sequence Analysis by Durbin et. al.
• Introduction to Bioinformatics by Arthur M. Lesk
• Beginning Perl for Bioinformatics by James Tisdall

Grading: 50% mid-term and 50% final exam

Course Overview: We will cover Perl programming, sequence alignment, and hidden Markov models (HMM). We will implement a pairwise sequence alignment program using dynamic programming, the Viterbi algorithm for HMM sequence alignment, and train program parameters on real data. If time permits we will also cover population structure identification using genome-wide SNP data.

Course plan:

Topic	Date	Remarks
Introduction	09/02/08	Slides
Perl basics	09/09/08	Slides Basic Unix command sheet
Pairwise sequence alignment in Perl	09/16/08
Subroutines, returning arrays and hashes, and sequence alignment in Perl; affine gaps	09/23/08	Slides Affine gaps Affine gaps (more notes)
Subroutines, local alignment, profile alignment	09/30/08	Slides Local alignment and BLAST Profile alignment
Profile and multiple alignment	10/07/08	Notes from Ron Shamir's course: (a) Pairwise alignment (b) Alignment heuristics
Mid-term exam	10/14/08
Hidden Markov models	10/21/08	Slides HMM notes from Ron Shamir's course gen_loaded_die.pl
Hidden Markov models and parameter estimation	10/30/08
Population structure identification	11/04/08	Slides
K-means clustering	11/11/08
K-means clustering in Perl	11/18/08
Classes follow a Thursday schedule (no class)	11/25/08
Review	12/02/08
Final exam	12/09/08