BNFO 235: Programming in Bioinformatics
Fall 2008

Instructor: Usman Roshan
Office: GITC 3802
Ph: 973-596-2872
Office hours: Monday 2:30-4pm and Thursday 11:30-2pm
Email: usman@cs.njit.edu

Recommended Text:

1. Beginning Perl for Bioinformatics by James Tisdall
2. Perl for Bioinformatics by Arun Jagota (available here both in print and ebook)
3. Introduction to Bioinformatics by Arthur M. Lesk

Grading: 80% weekly programming asssignments and 20% exam

Course Overview: We will cover the basics of Perl and implement programs for comparing DNA and protein sequences.

Course plan:

Topic	Date	Remarks
Background and Intro to Perl	09/02/08	Slides
Intro to Perl	09/08/08	Slides Basic Unix command sheet
Basic data types, I/O, Control structures	09/11/08
File I/O, String manipulation	09/15/08	HW 1
String manipulation	09/17/08	HW 2
Subroutines	09/22/08	Slides HW 3
Subroutines	09/25/08	HW 4
Pairwise sequence comparison	09/29/08	HW 5
Sequence alignment	10/02/08	HW 6
Sequence alignment	10/06/08	HW 7
BLAST	10/09/08	HW 8
Sequence alignment	10/13/08	HW 9
Sequence alignment	10/16/08	HW 10
Sequence alignment	10/20/08	HW 11
Sequence alignment	10/23/08
Genome-wide association studies	10/27/08	Slides HW 12
Genome-wide association studies	10/30/08
Contigency tables	11/03/08	HW 13
Odds ratios	11/06/08
SNP selection	11/10/08
SNP selection by odds ratios	11/13/08
SNP selection by odds ratios	11/17/08
SNP selection by odds ratios	11/20/08
Perl exercises	11/24/08
Perl exercises	11/25/08	HW 14
Perl exercises	12/01/08
Perl exercises	12/04/08
Final exam	12/08/08