Date

Topic

Assigned

Due

Jan 15

Bioinformatics overview; Syllabus; Unix, Perl and Editors

System Setup

Read Ch. 1-2

 

17

String Manipulation (Chapter 3)

HW 1

 

22

Regular Expressions (Chapter 4)

HW 2

HW 1
Solutions

24

Regex (Chapter 4), continued (plus some from Chapter 12)
Code for searching whole genome

HW 3
Text file for #2

HW 2
Solutions

29

Calculations and Randomness (Chapters 5 and 13)

 

 

31

Control Structures (Chapter 6)

HW 4

HW 3
Solutions

Feb 5

Control Structures, cont., and Subroutines (Chapter 7)
Nested loops code

HW 5

HW 4

7

Reading Files (Chapter 8) and Arrays (Chapter 9)

Review 1

HW 5

12

Arrays, cont.

 

 

14

Sequence analysis with EMBOSS (use dottup for dot plots)
dot plots & global sequence alignment
Local alignment with bl2seq executable and documentation

Project 1
Seq 1
Seq 2

Review 1

19

Web Forms and CGI

 

21

Local alignment and BLAST

 

 

26

Project Work Day

 

28

Project Presentations

Project 1

Mar 1-9

SPRING BREAK

Mar 11

Genes and promoters
ORF Finders at NCBI, SMS and EMBOSS
CpG islands paper and tools at EMBOSS
TESTCODE online tool and paper

 

13

Genes and promoters PWM Math Minute

HW 6

 

18

Sequence evolution models

 

HW 6

20

Phylogenetic trees

HW 7

 

25

HOLIDAY

27

Phylogenetic trees, cont.

 

HW 7

April 1

Comparative genomics

 

 

3

Comparative genomics GRIMM

Review 2
paper for #1
sequences for #4

 

8

Microarray data analysis

 

 

10

Microarray data analysis, cont.

 

Review 2
due Sat noon

15

Protein structure informatics

Project 2

 

17

RNA structure prediction

 

 

22

Project Work Day (no class)

 

24

Project Work Day (no class)

 

 

29

Project Presentations

 

Project 2

May 1

Wrap up, course evaluations

 

 

6

No Class

Final Exam

12

Exam due at 5:00 p.m.

 

Final Exam