Charles Hauser St. Edward’s University

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Genomics at St. Edward’s University

Course Overview

This research-based course provides junior and senior undergraduates the opportunity to work as a research team through a large-scale sequencing project, beginning with sample preparation at the Washington University St. Louis Genome Sequencing Center through sequence finishing and analysis. The research problem will involve sequencing portions of chromosome 4 (dot chromosome) from Drosophila mojavensis and comparison with that of D. melanogaster to discern patterns of genome organization related to control of chromatin structure and gene expression.

Implementation

The class is organized into two main sections. In the first half of the course students undertake a genomics-level sequencing problem by creating high quality sequence of a 40 kb fosmid clone from the Drosophila mojavensis "dot" chromosome in collaboration with the Washington University Genome Sequencing Center. In the second half of the course, students will annotate and characterize repeat sequences in a fosmid from D. virilis. Lecture and lab will be interspersed. Because this is primarily a laboratory course, make-up sessions are not possible.

Lessons Learned and Future Plans

Syllabus for Bioinformatics 3445

Texts:

There are no required textbooks. Most of the lectures will be from research articles and handouts. For non-molecular biologists, I highly recommend (really!) The Cartoon Guide to Genetics, by Larry Gonick & Mark Wheelis. All materials required for the course, announcements, reading assignments, etc. will be posted on Blackboard.

Some online references:

Genome Education Partnership: http://gep.wustl.edu/

Flybase: http://flybase.org/

Ensembl Genome Browser: http://www.ensembl.org/index.html

UCSC Genome Browser: http://gander.wustl.edu/

NCBI BLAST server: http://www.ncbi.nlm.nih.gov/blast/Blast.cgi

Drosophila Comparative Genomics: http://www.biostat.wisc.edu/~cdewey/fly_CAF1/

Student Responsibilities, Grading

Students’ progress will be assessed by the following means: (1) Reports in oral and written format for both the finishing and annotation projects, (2) Problem sets, (3) Class-led discussions covering Figures from papers utilized in the course, (4) Lab notebook detailing the problems encountered in finishing and annotation and the strategies employed to address these.

Recognizing that students may face unusual circumstances and require some flexibility in the course of the semester, each student will have a total of two free late days to use as s/he sees fit. Any homework/project turned in late will be penalized at the rate of 20% per late day. Under no circumstances will homework/project be accepted more than three days after its due date.

Grades will be assigned based on the following components:

  • Finishing report (paper and oral) 25%
  • Annotation report (paper and oral) 25%
  • Problem sets 15%
  • Class presentations 15%
  • Peer evaluations (finishing, annotation) 10%
  • Participation in discussions of class readings 10%


Grading will be on a straight scale as follows:

A: 100-90%; B: 89-80%; C: 79-70%; D: 69-60%; F: <60%


Lab Overview: Finishing / Analysis / Annotation

I anticipate that students will become familiar with:

  • Use of Phred/Phrap/Consed to assemble and evaluate sequence reads
  • Repeat Masker
  • Commonly used DNA data bases
  • BLAST, FASTA searches for homology
  • Genscan, Twinscan and other search tools
  • Clustal for comparative analysis
  • As time permits, we will explore comparative genomics approaches used in other systems.