BNFO 601: Foundations of Bioinformatics I
Fall 2017

Instructor: Usman Roshan
Office: GITC 4207
Ph: 973-596-2872
Office hours: MW 1-2:30, Tue 1-3
Email: usman@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: 25% two exams, 30% final exam, 20% assignments

Course Overview: We will cover Perl programming, sequence alignment, hidden Markov models (HMM), expected accuracy alignment, short read mapping, and genome alignment. We will implement several alignment analysis algorithms and related analysis programs in Perl, some in class and some in assignments.

Course plan:

Topic	Date	Notes
Pairwise sequence alignment and scoring matrices	09/11/17	Slides Images to go with first webex recorded lecture I1 I2 I3 I4 I5 Nature BLOSUM paper Pairwise alignment notes (Roshan '05) How to compute the alignment accuracy
Perl basics and pairwise sequence alignment in Perl	09/18/17	Perl slides Perl bioinformatics practice problems Basic Unix command sheet Instructions for AFS login
Affine gaps	09/25/17	Affine gaps Affine gaps Alignment notes from Ron Shamir's course at Univ. of Tel Aviv Affine gaps (pages 23 to 27) Affine gap (corrected) traceback Programming assignment #1 Affine gap alignment
Parameter selection by cross-validation	10/02/17	Parameter selection by cross-validation 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 Alignment accuracy script Programming assignment #2 Affine gap cross validation Affine Needleman-Wunsch in Perl (part 1) Affine Needleman-Wunsch in Perl (part 2) Affine Needleman-Wunsch in Perl (part 3) Cross-validation program for Needleman-Wunsch gap penalty
Local alignment, BLAST	10/10/17	Local alignment and BLAST Hands-on bioinformatics exercise DNA example input and output for Smith-Waterman alignment BLAST alignment heuristic Programming assignment #3 Affine and non-affine gap with BLOSUM62 cross validation
Profiles, multiple sequence alignment, and exam review	10/16/17	Multiple sequence alignment Profile alignment Multiple and local alignment notes (Roshan '05) Comparison of multiple alignment programs Midterm review sheet
First exam	10/23/17
Hidden Markov models	10/30/17	HMM slides HMM notes by Ron Shamir gen_dice_rolls.pl
HMM sequence alignment in Perl and parameter estimation by cross-validation	11/06/17	Programming assignment 4 HMM sequence alignment in Perl HMM sequence alignment code in Perl To run long jobs on OSL machines do krenew -t -K 30 -- sh -c 'command'
Expected accuracy sequence alignment	11/13/17	HMM alignment probability in Perl Baum welch exercise - computing expected values of HMM parameters Expected accuracy alignment MSAProbs and comparison of protein alignment programs BLOSUM 62 normalized counts BLOSUM 62 normalized counts (reformatted) Programming assignment 5 Posterior probabilities via HMM Forward backward probabilities in Perl (part 1) Forward backward probabilities in Perl (part 2) Forward backward probabilities in Perl (part 3) Forward backward probabilities in Perl (part 5)
Genome comparison and short read mapping	11/20/17	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 MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence 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 6 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, and metagenomics, and exam review	11/27/17	Genome alignment Slides by Mark Craven Papers on genome alignment: Comparative assessment of methods for aligning multiple genomes Alignathon Review sheeet
Exam 2	12/04/17
Whole genome alignment assignment (extra credit), exam 2 solution, and final review	12/11/17	Metagenomics: CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers Extra credit assignment Simulated dog chromosome Simulated rat chromosome True alignment of dog and rat Program to obtain accuracy from maf comparator output Final exam review sheeet
Final exam