Experimental Biology Lab: Comparative Genomics
Lecture: Introduction (Fredrik
- 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
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
- 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
4B. Lab: The
Accelrys Wisconsin Package and Pairwise Alignment and
- 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
Sequence Alignment (Steve Thompson)
- How do we align more than just two sequences at the
- 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
6B. Lab: NJ and Parsimony
- Use PAUP for neighbor joining and parsimony
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
8B. Lab: Phylogenetics III
- Use PAUP and MrBayes for post-tree analyses
9A. Lecture: Scientific Writing
9B. Lab: Writing a Project Proposal
- Worth 14% of grade
- On a chosen individual project
- Maximum two pages (single-spaced, excluding
- Proposal due Friday same week
10. Mandatory Project Counseling
- One-to-one counseling on the project
- Revised proposal due Friday same week
11. Mandatory Project Counseling
- One-to-one counseling on the revised project
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.