BNFO 236: Programming for Bioinformatics II
Spring 2017

Instructor: Usman Roshan
Office: GITC 3802
Ph: 973-596-2872
Office hours: Wed 1-4
Email: usman@njit.edu

Teaching Assistant: Xiaoyuan Liang
Office hours: By appointment only
Email: xl367@njit.edu

Recommended texts:
Grading: 10% weekly homework, 5% programming assignments, 25% two exams, and 35% final

Course Overview: We will implement several programs for sequence analysis. This includes the Needleman-Wunsch algorithm for optimal sequence alignment and UPGMA for constructing evolutionary trees.

Course plan:

Topic
Date
Remarks
Introduction: Python
01/17/17
Comparing DNA sequences 01/19/17
HW 1
Sequence alignment 01/24/17
Alignment notes
HW 1 solution
Random traceback to compute random alignments 01/26/17
HW 2
Needleman-Wunsch 01/31/17
Needleman-Wunsch slides
Functions 02/02/17
HW 3
Needleman-Wunsch and runtime analysis, BLOSUM62 02/07/17
Needleman-Wunsch slides
BLOSUM 62
Snow day - classes cancelled 02/09/17
Finding similar sequences in a database - Smith Waterman
02/14/17
Smith-Waterman alignment

HW 4

Horse Haemoglobin (PDB 2dhb)
Sequences from BLAST search
BLAST output
Global and local alignment scores with BLOSUM_62

Chicken Cytochrome bc 1 (PDB 3h1j)
Sequences from BLAST search
BLAST output
Global and local alignment scores with BLOSUM_62

Smith-Waterman 02/21/17
DNA example input and output for Smith-Waterman alignment
Smith Waterman in Python
BLAST-like alignment 02/23/17
BLAST alignment

E.coli K12 MG1655 genome
Related proteobacteria genomes
Bacterial phylogeny

NWscore alignment function in Python

Programming assignment 1
T-cell antigen receptor (PDB 1TCR)
Sequences from BLAST search

T-cell antigen receptor (PDB 1TCR)
Sequences from BLAST search
BLAST-like database search 02/28/17
BLAST-like database search and practice problems 03/07/17
Practice problems
Exam review and makeup class 03/08/17
First exam 03/09/17
Spring break 03/14/17
Spring break 03/16/17
Distance based phylogeny reconstruction 03/21/17
UPGMA
UPGMA algorithm, data structure to represent phylogenies 03/23/17
UPGMA implementation
Python function to make Newick tree

HW 5
UPGMA implementation in Python 03/28/17
HW 6
UPGMA implementation in Python and Newick format 03/30/17
Jukes Cantor distance matrix for Haemoglobin aligned sequences
Online phylogeny viewer
UPGMA in Python 04/04/17
UPGMA in Python 04/06/17
HW 7
Jukes Cantor distance matrices 04/11/17
UPGMA on simulated data 04/13/17 HW 8
Neighbor joining 04/18/17
Additional topics 04/20/17
Second exam review session 2:30 to 3:30 (Room TBA) 04/24/17
Second exam 04/25/17
Additional topics and final review 04/27/17
Final exam, FMH 108 2:30 to 5pm 05/11/17