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

Recommended Textbooks:
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:

Pairwise sequence alignment and scoring matrices
Perl basics and pairwise sequence alignment in Perl
Affine gaps 09/25/17
Parameter selection by cross-validation 10/02/17
Local alignment, BLAST
Profiles, multiple sequence alignment, and exam review 10/16/17
First exam
Hidden Markov models 10/30/17
HMM sequence alignment in Perl and parameter estimation by cross-validation 11/06/17
Expected accuracy sequence alignment 11/13/17
Genome comparison and short read mapping 11/20/17
Genome alignment, and metagenomics, and exam review 11/27/17
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