Course No. 3393.505
Biological Sequence Analysis

 

Interdisciplinary Bioinformatics Program, Seoul National University

Instructor
Prof. Byoung-Tak Zhang
TA:
Jang-Min Oh, jmoh@bi.snu.ac.kr, Tel.: 880-1847, Room 301-419 오장민 12월20일부터 4주간 자리 비웁니다. 보고서를 오장민에게 보내지 마세요... 절대로
엄재홍, [E-mail addr. was deleted for anti spam], Tel.: 880-1847, Room 301-419 (프로젝트1제출)
지성욱, swchi@cbit.snu.ac.kr, Tel.: 880-5890, Room 138-409 (프로젝트2제출)
 
Classroom
18-403
Time
Wednesday, 9:15-12:00
Textbook
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Richard Durbin. S. Eddy, A. Krogh, G. Mitchison.
Requirements
Two exams: 40 %, two projects: 40%, homeworks: 15%, class participation: 5%
    Project 1: Gene finding with probabilistic models
    Project 2: Analysis in RNA sequences with probabilistic models
Objectives
  • Understanding probabilistic models, particularly hidden Markov models (HMMs).
  • Understanding analysis of a wide variety of sequence analysis problems.

  • Schedule
Date Main Subjects
Week 1

 Introduction (Chap 1) [pdf slids (Slide A: COLOR, B/W) (Slide B: COLOR, B/W)]

Week 2

 Background on probability (Chap 11) [pdf slids COLOR, B/W]

Week 3

 Background on probability (Chap 11)

Week 4

 Pairwise alignment (Chap 2) [pdf slids COLOR, B/W]

Week 5
Week 6

 Markov chains and hidden Markov models (Chap 3) [pdf slids #1 COLOR, B/W][pdf slids #2 COLOR, B/W]

Week 7

 Assignment of Project (Project):
 HMM Tutorial, HMMER Tutorial

3d_darkbg_h_board.gifClick!

Week 8  Midterm Exam
Week 9

 Pairwise alignment using HMMs (Chap 4) [ppt slide: PPT]

Week 10
 Profile HMMs for sequence families (Chap 5) [ppt slide: PPT]
Week 11
 Project Midterm Presentations: Schedule
Week 12

 Multiple sequence alignment methods (Chap 6)[ppt slide: PPT]

Week 13
 Transformational grammars (Chap 9)
Week 14

 과제 발표

Week 15

 Final Exam(12월18일)


 보고서제출 마감(12월16일)


 

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