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Experimental Biology Lab: Comparative Genomics

Course Statement

The computer analysis of genetic information is increasingly vital for biological research and in applications ranging from drug development to nature conservation. This course aims to provide first-hand experience in this area. It begins with lectures introducing the genomics databases, the molecular biology behind the data, and the computational techniques used to analyze it. Concurrently, computer labs provide hands-on learning on searching the databases, analyzing the data, and using scientific literature. Each student finishes the semester by independently designing and executing an original research project, after which they submit a written paper and give a talk presenting their results.


What is Comparative Genomics?

What type of genomics databases are available?

  • sequence -- protein (e.g. SwissProt) and/or DNA (e.g. GenBank)
  • mapping -- linkage associations (where is the sequence in the genome?)
  • literature -- e.g. PubMed references

And how are they accessed?

  • often through a browser, e.g:
  • What is the molecular biology behind the analyses?

    • the Central Dogma: DNA --> RNA --> protein
    • complications: alternative splicing, RNA editing, prions, etc.
    • Homology: relationship by descent!

    What types of analyses are available?


    Grading

    The course consists of two parts: (1) an introductory part, during which we will introduce you to some tools that are used in comparative genomics and discuss the scientific method in general; and (2) a project part, during which you design, perform, and present a small comparative genomics research project.

    During the introductory part, you will have home assignments every week (8 in total). The assignments are due the following week and give 2 points each (total 16 points). During the project part you will first write a two-page project proposal before starting on your research. When you have completed your study, you write a 10-page scientific report. Finally, you present your project orally in front of the rest of the students. The project proposal can give you 14 points total, the project report 50 points, and the oral presentation 20 points, for a total maximum for the course of 100 points. These points are translated to grades as follows: 100-90 (A), 89-80 (B), 79-70 (C), 69-60 (D), 59-0 (F).

    It is essential that each proposal, report, and oral presentation contains a significant amount of original material. Copying material from other students or from the web without giving due credit to the original source will automatically result in an F grade for the course, in addition to other disciplinary actions that might be taken by FSU.

    See under 'Assignments' (link on the left side of this page) for more information on the grading expectations.

    Suggested Texts:

    We highly recommend the following texts, but do not require you to buy them.

    • Phylogenetic Trees Made Easy by Barry G. Hall; Sinauer Associates, Inc. Second edition.
    • Writing Papers in the Biological Sciences by Victoria E. McMillan; Bedford/St. Martin's. Third edition.

    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

    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.

    Attendance

    Attendance is compulsory the first day of the course (FSU policy). Attendance is also compulsory for the individual counseling session (on March 22) and the oral presentations the last day of the course (April 19). Attendance during the lectures and lab sessions is highly recommended but not mandatory. Lectures and lab tutorials will be made available on the course web site (on the FSU Blackboard system).

    ADA Statement

    Florida State University provides high-quality services to students with disabilities, and we encourage you to take advantage of them. Students with disabilities needing academic accommodations should:

    (a) register with, and provide documentation to, the Student Disability Resource Center (SDRC) in room 108 in the Student Services Building (644-9566); and
    (b) bring me a letter from SDRC indicating your needed academic accommodations. Please do this during the first week of class.
    For more information on this see the Resource Center's web site.

    Academic Honor code

    Students are expected to uphold the Academic Honor Code published in The Florida State University Bulletin and in the Student Handbook. The first paragraph says: The Academic Honor System of Florida State University is based on the premise that each student has the responsibility to uphold the highest standards of academic integrity in the student's own work.

 
   
 
© 2013 Steven M. Thompson, acknowledgements and thanks to the Florida State University Biology Department for generously extending Web hosting and e-mail services beyond my FSU tenure. stevet@bio.fsu.edu
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