BNFO 601: Foundations of Bioinformatics I
Fall 2018

Instructor: Usman Roshan
Office: GITC 4207
Ph: 973-596-2872
Office hours: T,W,Th: 2-3
Email: usman@njit.edu

Grader: Abdulrhman Aljouie
Email: aa547@njit.edu
Recommended Textbooks:
Grading: 25% two exams, 25% final exam, 25% 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
09/10/18
Perl basics and pairwise sequence alignment in Perl
09/17/18
Affine gaps 09/24/18
Parameter selection by cross-validation 10/01/18
Local alignment, BLAST
10/08/18
Profiles, multiple sequence alignment, and exam review 10/15/18
First exam
10/22/18
Hidden Markov models 10/29/18
HMM sequence alignment in Perl and parameter estimation by cross-validation 11/05/18
Expected accuracy sequence alignment 11/12/18
Genome comparison and short read mapping 11/19/18
Genome alignment, and metagenomics, and exam review 11/26/18
Exam 2 12/03/18
Whole genome alignment assignment (extra credit), exam 2 solution, and final review 12/10/18
Final exam