BNFO 135: Programming in Bioinformatics I
Fall 2011

Instructor: Usman Roshan
Office: GITC 3802
Ph: 973-596-2872
Office hours: T 1-3pm, Fri 12-2pm, and by appointment
Email: usman@cs.njit.edu

TA: Wei Wang
Office: GITC 3802
Office hours: Tue, Wed, Thu, 1-3pm, and by appointment
Email: ww42@njit.edu

Recommended Text:
  1. Bioinformatics Programming Using Python by Mitchell Model

Grading: 15% weekly programming asssignments, 25% two exams, and 35% final

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

Course plan:

Topic
 Date
 Remarks
Background and Intro to Python
 09/02/11
 Basic molecular biology
Intro to Python
Input and output, lists 09/06/11
 See previous slides
HW 1
If-else statements 09/09/11
 See slides from first lecture
HW 2
For and while loops 09/13/11
 See slides from first lecture
HW 3
More loops
 09/16/11
 HW 4
More loops
 09/20/11
 HW 5
Codon to amino acid map
Dictionaries
 09/23/11
 HW 6
mRNA translation
 09/27/10
 HW 7
Searching for sequences
 09/30/11
 HW 8
Review
 10/04/11
 Practice problems for exam 1
First exam
 10/07/11
Exam solution and sequence alignment 10/11/11
 Sequence alignment
HW 9
Sequence alignment score
 10/14/11
 HW 10
Hands-on bioinformatics exercise
Split method 10/18/11
 HW 11
Conserved columns 10/21/11
 Trypsin alignment in FASTA
HW 12
Conserved columns
 10/25/11
 HW 13
Conserved columns
 10/28/11 HW 14
Converting between data formats
 11/01/11 FASTA and PHYLIP formats
HW 15
Converting between data formats
 11/04/11 HW 16
Extension gaps
 11/08/11 HW 17
Affine (extension) gaps
Review
 11/11/11 Practice problems
Exam 2
 11/15/11
Exam 2 solution
 11/18/11 HW 18
Exam 2 solution
 11/22/11 No office hours today
Substring alignment problem
Genome assembly problem
Scoring sequence alignment
 11/29/11
Extension gaps 12/02/11
Extra credit assignment 12/06/11 Extra credit assignment
BLOSUM 62 scoring matrix
Review 12/09/11
Final exam 12/16/10 TIER 104 8:30am to 11am