BNFO 601: Foundations of Bioinformatics I
Fall 2012

Instructor: Usman Roshan
Office: GITC 3802
Ph: 973-596-2872
Office hours: Mon and Wed 2:30-4pm, Thu 2-4pm, and by appointment
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
• Introduction to Machine Learning by Ethem Alpaydin

Grading: 25% two exams, 35% final exam, 15% three projects

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 and the Viterbi algorithm for HMM sequence alignment. We will also cover genome-wide association studies.

Course plan:

Topic	Date	Notes
Pairwise sequence alignment and scoring matrices	09/06/12	Slides Nature BLOSUM paper Pairwise alignment notes (Roshan '05) How to compute the alignment accuracy
Perl basics and pairwise sequence alignment in Perl	09/13/12	Perl slides Basic Unix command sheet Instructions for AFS login
Optimal sequence alignment in Perl	09/20/12
Affine gaps	09/27/12	Alignment notes from Ron Shamir's course at Univ. of Tel Aviv Affine gaps Programming assignment Affine gap alignment
Parameter selection by cross-validation	10/04/12	Parameter selection by cross-validation Alignment accuracy script BAliBASE 3.0 reference alignments PREFAB pairwise reference alignments Train datasets Test datasets Simple substitution score matrix BLOSUM 62 matrix
Local alignment, BLAST, and review for exam	10/11/12	Local alignment and BLAST
First exam	10/18/12
Profile alignment, multiple sequence alignment, and BLAST exercise	10/25/12	Hands-on bioinformatics exercise Profile alignment Multiple and local alignment notes (Roshan '05) Comparison of multiple alignment programs
NJIT closed due to hurricane Sandy	11/01/12
Exam 1 solution, short read mapping	10/25/12	Slides Papers on short read alignment: BFAST: An Alignment Tool for Large Scale Genome Resequencing Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads A survey of sequence alignment algorithms for next-generation sequencing Detecting structural variations in the human genome using next generation sequencing Mapping and sequencing of structural variation from eight human genomes Split function in Perl Programming assignment 2 Chromosome 22 Reads of divergence .01 Reads of divergence .05 Reads of divergence .1 Reads of divergence .15 Reads of divergence .2 Reads of divergence .25
Hidden Markov models	11/15/12	HMM slides HMM notes by Ron Shamir gen_dice_rolls.pl
HMMs	11/20/12
Second exam	11/29/12
Second exam solution and extra credit assignment	12/06/12	Extra credit assignment Alignment accuracy Perl script PREFAB pairwise reference alignments Alignments for training
Final exam	12/20/12	GITC 2400, 6-8:30pm