BNFO 136: Programming for Bioinformatics II
Spring 2012

Instructor: Usman Roshan
Office: GITC 3802
Ph: 973-596-2872
Office hours: Mon and Wed 1 to 3, and Tue 4 to 5:30
Email: usman@cs.njit.edu

Recommended texts:

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

Grading: 15% weekly programming asssignments, 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	01/18/12	Slides 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	01/23/12	Slides HW 1
Sequence alignment	01/25/12	Alignment notes Affine gaps HW 2
Random traceback to compute random alignments	01/30/12	HW 3
Functions	02/01/12	HW 4
Needleman-Wunsch	02/06/12	Needleman-Wunsch slides HW 5
Needleman-Wunsch	02/08/12	HW 6
Finding similar sequences	02/13/12	HW 7
Finding similar sequences in a database	02/15/12	HW 8
Review for first exam	02/20/12
First exam	02/22/12
Exam solution and BLAST like alignment	02/27/12
Smith-Waterman local alignment	02/29/12	Smith-Waterman alignment slides
Alignment with BLOUSM_62 substitution matrix, local alignment, and database search	03/05/11	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 HW 9
BLAST alignment and programming assignment as extra credit for first exam	03/07/11	Extra credit programming assignment #1 BLOSUM_62 matrix
Spring break	03/12/12
Spring break	03/14/12
Distance based phylogeny reconstruction, UPGMA	03/19/12	UPGMA HW 10
UPGMA	03/21/12	HW 11
UPGMA	03/26/12
UPGMA in Python	03/28/12	Query for extra credit assignment Database for extra credit assignment BLAST output Correct answer
UPGMA in Python	04/02/12
UPGMA in Python and newick format for trees	04/04/12	HW 12
Jukes Cantor evolutionary distances	04/09/12	Jukes Cantor distances Haemoglobin sequences (SWISSPROT species IDs) Haemoglobin aligned sequences Online phylogeny viewer HW 13
Calculating distance matrices and UPGMA trees from unaligned sequences	04/11/12
Neighbor joining algorithm, second exam review	04/16/12	Neighbor joining
Second exam	04/18/12
Neighbor joining in Python	04/23/12
NJ in Python	04/25/12
Final exam review	04/30/12
Final exam	05/07/12