Experimental Biology Lab: Comparative Genomics

Contents

1A. Lecture: Introduction (Fredrik Ronquist)

• Introduction to the course: schedule, what is required, grades, computational
  and other resources needed for the project, practical arrangements etc.
• What is comparative genomics?
• Introduction to the scientific method

1B. Lab: Introduction to Linux

• Logging in
• Using the Linux GUI
• Using the command line interface
• Printing from the Linux machines

2A. Lecture: Library Resources at FSU (Presented by Michael Luesebrink)

• Scientific publishing
• What library resources are available at FSU?
• How do I access these resources?
• How do I find the information I need?
• How do I cite the information I find in my own research papers?

2B. Lab: Literature Searching

• Searching for literature references
• Getting copies of papers
• Managing references using RefManager
• Producing bibliographies

3A. Lecture: Genomics Web Resources (Steve Thompson)

• What web databases and resources are available for genomic research?
• How do I get scientific literature references?
• How do I find medical implications?
• How do I find gene mapping information?
• How do I get 3D structures of biological molecules?
• What web tools are available for genomic comparisons and gene finding?
• Introduction to the Accelrys Wisconsin Package (a k a the Genetics Computer Group - GCG)

3B. Lab: Genomics Databases and Tools

• Using Web interfaces to genomics analyses,
  including genomic comparisons and gene finding.

4A. Lecture: Similarity Searching and Pairwise Alignment (Steve Thompson)

• How do you discover sequence similarity and what is dynamic programming?

4B. Lab: The Accelrys Wisconsin Package and Pairwise Alignment and Searching

• Introduction to GCG and the local databases hosted by Mendel on FSU campus
• Searching for sequences based on sequence similarity: BLAST and FASTA
• Find sequence data for a comparative project

5A. Lecture: Multiple Sequence Alignment (Steve Thompson)

• How do we align more than just two sequences at the same time?

5B. Lab: Multiple Sequence Alignment

• Multiple alignment and analysis using GCG
• Multiple alignment using ClustalW

6A. Lecture: Phylogenetics I (Fred Ronquist)

• Introduction to phylogenetics
• Distance methods: UPGMA and Neighbor Joining
• Parsimony

6B. Lab: NJ and Parsimony

• Use PAUP for neighbor joining and parsimony analyses

7A. Lecture: Phylogenetics II (Fred Ronquist)

• Statistical inference principles
• Maximum likelihood inference of phylogeny
• Bayesian inference of phylogeny

7B. Lab: Phylogenetics II

• Use PAUP for ML analyses
• Use MrBayes for Bayesian analyses

8A. Lecture: Phylogenetics III (Fred Ronquist)

• Reconstructing ancestral states
• Identifying mutations / substitutions
• Historical biogeography
• Classification

8B. Lab: Phylogenetics III

• Use PAUP and MrBayes for post-tree analyses

9A. Lecture: Scientific Writing

• Scientific publishing
• How to write a research paper
• An example from the Group Project: Sex Determination in Primates: the SRY Locus
• How to write a proposal for the Individual Project.

9B. Lab: Writing a Project Proposal

• Worth 14% of grade
• On a chosen individual project
• Maximum two pages (single-spaced, excluding references)
• Proposal due Friday same week

10. Mandatory Project Counseling

• One-to-one counseling on the project proposal
• Revised proposal due Friday same week

11. Mandatory Project Counseling

• One-to-one counseling on the revised project proposal

12-14. Work on Individual Project

14. Written Report Due

• Worth 50% of grade
• Between ten and twenty pages (double-spaced, excluding figure(s) and table(s))
• Will be returned graded the following week

15. Oral Presentation

• Worth 20% of grade.
• Maximum eight minutes per student
• Will be graded same week.