BNFO 601: Foundations of Bioinformatics I
Fall 2014

Instructor: Usman Roshan
Office: GITC 3802
Ph: 973-596-2872
Office hours: Tue 4-5:30, Wed 2-5
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, 30% final exam, 20% 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	09/04/14	Slides Nature BLOSUM paper Pairwise alignment notes (Roshan '05) How to compute the alignment accuracy
Perl basics and pairwise sequence alignment in Perl	09/11/14	Perl slides Basic Unix command sheet Instructions for AFS login
Affine gaps	09/18/14	Alignment notes from Ron Shamir's course at Univ. of Tel Aviv Affine gaps (pages 23 to 27) Programming assignment #1 Affine gap alignment
Parameter selection by cross-validation	09/25/14	Parameter selection by cross-validation BAliBASE 3.0 reference alignments PREFAB pairwise reference alignments Train datasets Test datasets Simple substitution score matrix BLOSUM 62 matrix
Local alignment, BLAST, and exam review	10/02/14	Perl bioinformatics practice problems Local alignment and BLAST Hands-on bioinformatics exercise DNA example input and output for Smith-Waterman alignment BLAST alignment heuristic Programming assignment #2 Affine gap cross validation Alignment accuracy script
Profiles and multiple sequence alignment	10/09/14	Multiple sequence alignment Profile alignment Multiple and local alignment notes (Roshan '05) Comparison of multiple alignment programs
First exam	10/16/14
Hidden Markov models	10/23/14	HMM slides Profiles HMM notes by Ron Shamir gen_dice_rolls.pl
HMM sequence alignment in Perl and parameter estimation by cross-validation	10/30/14	Programming assignment #3 HMM sequence alignment in Perl HMM sequence alignment code in Perl
Expected accuracy sequence alignment	11/06/14	Programming assignment #3 for undergrads HMM alignment probability in Perl Baum welch exercise - computing expected values of HMM parameters Baum welch exercise Expected accuracy alignment
Genome comparison and short read mapping	11/13/14	Slides Papers on short read alignment: Tools for mapping high-throughput sequencing data BFAST: An Alignment Tool for Large Scale Genome Resequencing Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads NextGenMap: fast and accurate read mapping in highly polymorphic genomes Fast GPU solutions for accurate mapping of divergent reads Detecting structural variations in the human genome using next generation sequencing Fine-scale structural variation of the human genome Mapping and sequencing of structural variation from eight human genomes Split function in Perl Programming assignment 4 Mapping short reads to a genome 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
Genome alignment	11/20/14	Genome alignment Slides by Mark Craven Papers on genome alignment: Comparative assessment of methods for aligning multiple genomes Alignathon Review sheeet
Exam 2	11/25/14
Exam 2 solution and final review	12/04/14
Final exam