BNFO 136: Programming for Bioinformatics II
Spring 2014

Instructor: Usman Roshan
Office: GITC 3802
Ph: 973-596-2872
Office hours: Tue and Fri 4 to 5:30 and by appointment
Email: usman@cs.njit.edu

Teaching Assistant: Mohammedreza Esfandiari (Payam)
Office hours: By appointment
Email: me76@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
School closed due to snow	01/21/14
Introduction: Python	01/24/14	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	01/28/14	HW 1
Sequence alignment	01/31/14	Alignment notes HW 2
Random traceback to compute random alignments	02/04/14	HW 3
Functions and random traceback	02/07/14	HW 4
Functions	02/11/14	HW 5
Needleman-Wunsch and runtime analysis	02/14/14	Needleman-Wunsch slides HW 6
Needleman-Wunsch implementation	02/18/14	HW 7
Needleman-Wunsch and finding similar sequences in a database	02/21/14	HW 8
Finding similar sequences in a database	02/25/14	HW 9 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 searh BLAST output Global and local alignment scores with BLOSUM_62
BLAST-like database search and first programming assignment	02/28/14	HW 10 Programming assignment 1 E.coli K12 MG1655 genome Related proteobacteria genomes Bacterial phylogeny
BLAST-like database search	03/04/14
BLAST-like database search and exam review	03/07/14
First exam	03/11/14
First exam solution and distance based phylogeny reconstruction	03/14/14	UPGMA
Spring break	03/18/14
Spring break	03/21/14
Distance based phylogeny reconstruction, UPGMA	03/25/14	UPGMA HW 11
UPGMA algorithm, data structure to represent phylogenies	03/28/14	UPGMA implementation Python function to make Newick tree HW 12
UPGMA implementation in Python	04/01/14	HW 13
UPGMA implementation in Python	04/04/14
UPGMA implementation in Python	04/08/14	HW 14
UPGMA implementation in Python	04/11/14	HW 15 Jukes Cantor distances Haemoglobin sequences (SWISSPROT species IDs) ClustalW webserver Haemoglobin aligned sequences Jukes Cantor distance matrix for Haemoglobin aligned sequences Online phylogeny viewer
Phylogenies from whole genome sequences	04/15/14	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 HW 16
Good Friday	04/18/14
Second exam review	04/22/14
Second exam	04/25/14
Neighbor joining algorithm	04/29/14	Neighbor joining Model tree (phylogram) Model tree (Newick text) Simulated data divergence .1 Simulated data divergence 1 Simulated data divergence 10 Simulated data divergence 100 HW 17
Construction of phylogenies from raw unaligned sequences	05/02/14	Programming assignment 2 Model tree (phylogram) Model tree (Newick text) Haemoglobin sequences (SWISSPROT species IDs) Haemoglobin aligned sequences Jukes Cantor distance matrix for Haemoglobin aligned sequences Online phylogeny viewer
Final exam review	05/06/14