BNFO 601: Foundations of Bioinformatics I
Fall 2013

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	09/05/13	Slides Nature BLOSUM paper Pairwise alignment notes (Roshan '05) How to compute the alignment accuracy
Perl basics and pairwise sequence alignment in Perl	09/12/13	Perl slides Basic Unix command sheet Instructions for AFS login
Traceback and affine gaps	09/19/13	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	09/26/13	Parameter selection by cross-validation Alignment accuracy script Needleman-Wunsch in Perl (part 1) Needleman-Wunsch in Perl (part 2) BAliBASE 3.0 reference alignments PREFAB pairwise reference alignments Train datasets Test datasets Simple substitution score matrix BLOSUM 62 matrix
Gap selection by cross-validation	10/03/13	Perl bioinformatics practice problems
Local alignment, BLAST, and exam review	10/10/13	Local alignment and BLAST Hands-on bioinformatics exercise DNA example input and output for Smith-Waterman alignment BLAST alignment heuristic
First exam	10/17/13
Cross validation for affine gaps	10/24/13	Programming assignment #2 Affine gap cross validation Single gap cross validation for Needleman-Wunsch Affine alignment part 1 Affine alignment part 2 Train datasets Test datasets
Profiles and multiple sequence alignment	10/31/13	Multiple sequence alignment Profile alignment Multiple and local alignment notes (Roshan '05) Comparison of multiple alignment programs
Hidden Markov models	11/07/13	HMM slides HMM notes by Ron Shamir gen_dice_rolls.pl
HMM sequence alignment in Perl	11/14/13
Expected accuracy sequence alignment and genome wide association studies	11/21/13	Expected accuracy alignment GWAS
Genome comparison and short read mapping	11/26/13	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 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 A survey of sequence alignment algorithms for next-generation sequencing How to map billions of short reads onto genomes Papers on genome alignment: Slides by Mark Craven Comparative assessment of methods for aligning multiple genomes Split function in Perl Programming assignment 4 (meant as an exercise and not to be submitted for grading) 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
Second exam	12/05/13