BNFO 236: Programming for Bioinformatics II
Spring 2016

Instructor: Usman Roshan
Office: GITC 3802
Ph: 973-596-2872
Office hours: Tue and Thu 2:30 to 5 and by appointment
Email: usman@cs.njit.edu

Teaching Assistant: Ling Zhong
Office hours: By appointment
Email: lz25@njit.edu

Recommended texts:

• Introduction to Bioinformatics by Arthur M. Lesk
• Python Scripting for Computational Science by Hans Petter Langtangen

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	01/19/16	Slides (pdf) Python docs and sections to read An Informal Introduction to Python if Statements Reading and Writing Files Dictionaries for Statements Python download and installation System Basic Unix command sheet Instructions for AFS login
Comparing DNA sequences	01/22/16	HW 1
Sequence alignment	01/26/16	Alignment notes
Random traceback to compute random alignments	01/28/16
Functions and random traceback	02/02/16
Functions	02/04/16	HW 2
Needleman-Wunsch and runtime analysis, BLOSUM62	02/09/16	Needleman-Wunsch slides HW 3 BLOSUM 62
Finding similar sequences in a database - Smith Waterman	02/11/16	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	02/16/16	DNA example input and output for Smith-Waterman alignment BLAST alignment
BLAST-like database search	02/18/16	E.coli K12 MG1655 genome Related proteobacteria genomes Bacterial phylogeny Programming assignment 1
Evaluation of protein alignments	02/23/16	Alignment accuracy How to compute alignment qscore Qscore for evaluating alignments BAliBASE 3.0 reference alignments PREFAB pairwise reference alignments Train datasets Test datasets
	02/25/16	HW 5
First exam review	03/01/16
First exam	03/03/16
Distance based phylogeny reconstruction	03/08/16	UPGMA HW 6
UPGMA algorithm, data structure to represent phylogenies	03/10/16	UPGMA implementation Python function to make Newick tree HW 7
UPGMA implementation in Python	03/22/16
UPGMA implementation in Python and Newick format	03/24/16	Jukes Cantor distance matrix for Haemoglobin aligned sequences Online phylogeny viewer HW 8
Class cancelled	03/29/16
Jukes Cantor distance matrices	03/31/16	HW 9 Jukes Cantor distances Haemoglobin sequences (SWISSPROT species IDs) ClustalW webserver Haemoglobin aligned sequences Jukes Cantor distance matrix for Haemoglobin aligned sequences Online phylogeny viewer
UPGMA on simulated data	04/05/16	HW 10 Model tree (phylogram) Model tree (Newick text) Simulated data divergence .1 Simulated data divergence 1 Simulated data divergence 10 Simulated data divergence 100 E.coli K12 MG1655 genome Related proteobacteria genomes Bacterial phylogeny
Phylogenies from whole genome sequences	04/07/16	HW 11 Whole genome prokaryotic phylogeny Whole-Genome-Based Phylogeny and Divergence of the Genus Brucella Construction of a Phylogenetic Tree of Photosynthetic Prokaryotes Based on Average Similarities of Whole Genome Sequences Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices
Neighbor joining	04/12/16	HW 12 Neighbor joining
Class cancelled due to regional power outage	04/14/16
Second exam review	04/19/16
Second exam	04/21/16
Second exam solution	04/26/16
Additional topics: Bootstrapping phylogenies	04/28/16	Bootstrapping phylogenies Programming assignment 2
Final exam	05/09/16