Reading Material

55:195:01

Comp. Methods in Molecular Biology

Week 1 - Overview and Computing Concepts (I)

Lecture Notes

• Lecture Notes 1 (Casavant)

• Lecture Notes 1 (6 slides/page)

 

Useful Web sites

• CLCG homepage
• Guide to online information on the human genome

Book Recommendations

• Bioinformatics: Sequence and Genome Analysis

Week 2 - Bioinformatics Overview and Computing Concepts (II)

Lecture Notes

• Lecture Notes 2 (Casavant)

• Lecture Notes 2 (6 slides/page)

 

Demo:

• How to login Ski

 

Week 3 - Review of Molecular Biology and Genetics

Lecture Notes

• Lecture Notes Week 3 (Scheetz)

• Lecture Notes Week 3 (6 slides/page)

Week 4 - Sequence Analysis Algorithms

Lecture Notes

• Lecture Notes Week 4 (Casavant)

• Lecture Notes Week 4 (6 slides/page)

Demo

• Alignment Demo
• DotPlots
• HMMER
• Instruction of cluster

 

Week 5 - Programing Languages for Bioinformatics:  Perl

Lecture Notes

• Lecture Notes Week 5 (Scheetz)

• Lecture Notes Week 5 (6 slides/page)

Demo

• Bos Taurus Example
• BLAST Example

Week 6 - The CGI and BioPerl Modules

Lecture Notes

• Lecture Notes Week 6 (Bair)

• Lecture Notes Week 6 (6 slides/page)

Demos

• Perl Examples
• VI tutorial
• VI command reference

Homework

• Homework #1 (Hint added - March 7, 2003)

Week 7 - Biological Databases and Data structures

Lecture Notes

• Lecture Notes Week 7(Bair)

• Lecture Notes Week 7(6 slides/page)

Demos

• Examples for CGI and Database lectures

Homework

• Homework #2

• Homework #2 TIPS

Week 8 - Phylogenetics and Midterm*

Lecture Notes

• Lecture Notes Week 8(Scheetz)

• Lecture Notes Week 8(6 slides/page)

Week 9 – Spring Break

Week 10 - Hidden Markov Models and Domain Finding

• Lecture Notes Week 10(Casavant)

• Lecture Notes Week 10(6 slides/page)

Week 11 - Genome and Transcriptome Analysis

• Lecture Notes Week 11(Casavant)

• Lecture Notes Week 11(6 slides/page)

Homework

• Homework #3

• C source code for Global Alignment
• Perl source code for Global Alignment

Demo

• HMMER

Week 12 - Promoter and mRNA prediction

• Lecture Notes Week 12(Bair)

• Lecture Notes Week 12(6 slides/page)

Week 13 - Microarray and Gene Expression Analysis

• Lecture Notes Week 8(Scheetz)

• Lecture Notes Week 8(6 slides/page)

Week 14 - Pathways

• Lecture Notes Week 14(Bair)

• Lecture Notes Week 14(6 slides/page)

Week 15 - Linkage Analysis

• Lecture Notes Week 15(Braun)

• Lecture Notes Week 15(6 slides/page)

Week 16 - Gene/EST Mapping

• Lecture Notes Week 16(Scheetz)

• Lecture Notes Week 16(6 slides/page)