CS641-2C

Bioinformatics II

Department of Computer and Information Sciences

Tuesday - Thursday

3 semester hours credit

11:00 A.M. - 12:15 P.M.

Spring Semester 2005

 

Course Instructor:  Zhijie Guan

Phone Number: 934-5840

Email: guanz (at) cis.uab.edu

Office Hour: Tu. Thu. 2pm- 4pm or by appointment

 

Course Homepage: http://www.cis.uab.edu/cs641

 

Prerequisites: CS640 Bioinformatics I. Graduate standing, approved background in a biological science and permission of course lecturer. The following experiences are not necessary but highly recommended.

□       Artificial Intelligence course in undergraduate level

□       Algorithm, Data structure and/or Combinatorial mathematics

□       A programming language course

□       A little bit statistic and probabilistic knowledge

 

Textbook: Biological sequence analysis: Probabilistic models of proteins and nucleic acids. R. Durbin, S. Eddy, A. Krogh, and G. Mitchison. ISBN: 0521629713. Cambridge University Press. 1999.

 

Classroom: CH145

 

Course Description

This course is the second of a two-course sequence CS640/CS641 that is designed to introduce selected topics in bioinformatics with particular focus on computational challenges. The goal of this course is to introduce fundamental Bioinformatics algorithms and applications to the students. This course will cover three broad areas: (i) sequence analysis methods, (ii) phylogeny inference approaches, and (iii) microarray data analysis.

 

Grading Policy

Quizzes (11)

40%

Homework (3)

30%

Term Project

Project Presentation

10%

Project Report

20%

Notes:

1.      Student can drop off one of the lowest scores of the quizzes.

2.      The overall scores will NOT be curved.

 

Late Submission

All homework assignments are due at 5pm CST on the due date. Any assignment turned in after this deadline is considered late. Late assignments will lose 10% for every 24-hour period, up to a maximum of 50% (weekends and holidays count as one 24-hour period). All homework assignments should be submitted electronically via email. Please CC to yourself when you submit your assignments.

 
Class Conduct
  1. Students are expected to conduct themselves in a professional manner.
  2. Laptops will be allowed only for the purpose of the class. If a student uses the laptop for some other purposes and the misuse distracts other students, then that student's overall grade will be greatly affected.
  3. Students must turn their cell phones/pagers OFF during the class.

 

Class Attendance
  1. Attendance is mandatory for this course. If you know you will be absent for a legitimate reason, let the instructor know. If you are sick bring a doctor's excuse or a written university excuse to resolve the absences. An absence has to be resolved as soon as possible - otherwise it will not be treated as an excused absence.
  2. Students auditing this course are expected to attend the lectures. Auditing students with more than three unexcused absences will receive a failing grade.
  3. There will be NO make-ups for tests. A student anticipating an excused absence from a test should make arrangements in advance to sit for the exam at another time.

 

Academic Honesty

Students who plagiarize a computer program (or parts of a program), get others to write a program (or parts of a program), copy some else’ idea and words without correct references, or are found cheating on a quiz/exam, will be reported for academic dishonesty. Anyone who is caught cheating will receive a 0 on a given test or assignment. If a second offense occurs, the student will receive an F in the class. This includes both the provider of the information as well as the receiver of the information. Any student who violates the university's academic honesty policy will be reported for academic discipline. All university and department policies related to students are included here by implication.

 

E-mail

Every student will be required to use his/her official email address that is blazerid@uab.edu. New students must login and configure their email addresses. For more details on obtaining blazerid and configuring email please see: http://www.uab.edu/blazerid. All email communications will be made using this address. Additional instructions or announcements will be sent by e-mail, so check your mail often - at least twice a day (once in the morning and once at night). Also check the course webpage for up-to-date information and announcements. Instructor will check email frequently, so e-mail is often the best way to contact the instructor.

 

Course Schedule

 

Week

Date

Content

Note

Week 1

Jan. 4

Course Introduction

 

 

Jan. 6

Basic Introduction to Bioinformatics

 

Week 2

Jan. 11

Pairwise Alignment, Dynamic Programming

 

 

Jan. 13

Pairwise Alignment, Dynamic Programming

Quiz 1

Week 3

Jan. 18

Scoring Matrices, Significance of Scores, Introduction to BLAST

 

 

Jan. 20

Analysis of BLAST

Quiz 2, Assignment 1 out

Week 4

Jan. 25

Multiple Sequence Alignment & ClustalW

 

 

Jan. 27

Introduction to Hidden Markov Model

Quiz 3

Week 5

Feb. 1

Introduction to Hidden Markov Model

 

 

Feb. 3

Introduction to Hidden Markov Model

Quiz 4

Week 6

Feb. 8

Gene Finding

 

 

Feb. 10

Video on Nucleotide and Protein Sequence Analysis I

 

Week 7

Feb. 15

Video on Introduction to Phylogeny Inference

Out of town, Assignment 1 turn in

 

Feb. 17

Multiple Sequence Alignment & Profile HMM

Quiz 5

Week 8

Feb. 22

Systematics and Character Coding

 

 

Feb. 24

MSA & Phylogenetic Tree

 

Week 9

Mar. 1

Talks for assignment 1

Quiz 6, Assignment 2 out

 

Mar. 3

Phylogeny Inference: Maximum Parsimony

 

Week 10

Mar. 8

Phylogeny Inference: Maximum Parsimony

Phylogeny Inference: Maximum Likelihood

Quiz 7, Term Project Topics out

 

Mar. 10

Phylogeny Inference: Maximum Likelihood

 

Week 11

Mar. 15

Sankoff Algorithm

Quiz 8, Assignment 2 Question 1 and 2 turn in

 

Mar. 17

Felsenstein Zone and Distance introduced

Assignment 3 out

Week 12

Mar. 22

Distance & Likelihood

Quiz 9, Term Project Abstract due

 

Mar. 24

Tree Searching

Assignment 2 Question 3 turn in

Week 13

Mar. 29

 

Spring Break

 

Mar. 31

 

Spring Break

Week 14

Apr. 5

To be arranged

Out of town

 

Apr. 7

To be arranged

Out of town

Week 15

Apr. 12

Microarray data analysis

Quiz 10

 

Apr. 14

RNA Secondary Structure Prediction

Quiz 11

Week 16

Apr. 19

Project Presentation

Assignment 3 turn in

 

Apr. 21

Project Presentation

 

Week 17

Apr. 26

No Class

 

 

Apr. 28

Final Exam 10:45am - 1:15pm

 

 

 

Back to the Course Homepage