Christopher Smith San Francisco State University

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Genomics at San Francisco State University

Course Overview

BIOL638/738 is an introduction to basic bioinformatics principles, resources, and methods for graduate students. Students taking this class will get a broad overview of online database and tools for many day-to-day bioinformatics analyses. Using genome annotation as a central organizing principal, students will gain the ability to find and evaluate the quality of genomic data and use it to generate their own novel genome annotations for a sequence being studied. Students will be introduced to basic principles of data organization, hands-on software use, and bioinformatics analysis design including basic Unix skills, introductory Perl, and methodologies to retrieve and integrate bioinformatics data into coherent genome annotations that can be used to address relevant biological questions.


Lessons Learned and Future Plans

Syllabus for Bio 638/738 Bioinformatics & Genome Analysis

Student Learning Objectives:

  1. To gain familiarity with command-line OS X UNIX.
  2. To gain an understanding of the principles behind and execution of various genome analysis programs to detect repeats, similarity, and predict genes.
  3. To gain experience integrating and evaluating multiple types of computational evidence into a single coherent gene model or sequence feature
  4. To distill your results into concise data files for upload and inclusion in a peer-reviewed publication.
  5. To get experience writing and presenting a 10-minute summary of your semester’s work.

Course Work & Grading

Grading - 300 points total

Assignments (5 x 20 points) = 100
Attendance & Class participation = 50
Final Project = 150

There will be no make-up assignments or projects. Extra credit assignments may be available at the discretion of the instructor.


There will be five assignments that will be given in class that might include reading and critiquing a short research paper, presenting articles from the popular press that involve bioinformatics, performing more in-depth research for a gene or topic of interest, or executing a specific computational analysis.


• O’Reilly BLAST (ISBN: 1600330312)
• Scientific journal manuscripts and PDFs will be assigned in class.
• Web-based and UNIX readings will be assigned in class.

Course Scheule