FRS 002V —
Sec. 001 —
(2 units) — CRN 53619 — F 10:00-11:30am— 3132 Tupper
Comparing Mammalian Genomes
Instructor: Michael Syvanen, Department of Microbiology
& Immunology,
School of Medicine
Description: Comparative genomics concerns the comparison of
DNA sequences of very large regions of genomes. Today there is available large
tracts of sequences that remains unanalyzed. This course will begin
with a formal
presentation that defines the basic elements of the genome and the
types of evolutionary
questions that can be addressed from comparisons. Students will be assigned a
region of the mammalian genome with a goal of comparing and interpreting those
comparisons. This is a computationally intense endeavor so analysis
of sequences
will be carried out either at special websites or from local servers using unix
commands. I would expect that the students interested in this seminar to have
a good computational background, with or without much biology. These students
will learn some basic biology and will be exposed to a number of
basic computational
problems and how these problems are expressed in the real world of comparative
biology. The types of problems that are tackled by the individual students will
depend on their previous computer skills. Though any of the problems
can be worked
on at appropriate websites, more advanced analysis is possible with
some the ability
to work in unix with programming skills. Each student will come out
of this with
an enhanced understanding of inheritance and they will be exposed to
a real research
problem - what is a hypothesis and how computers can be applied to
solving scientific
questions. All students will be exposed for the first time to the
problem of handling
and organizing large complex databases.
Format: The instructor will meet with the students two hours
each week, perhaps longer for some who have weaker backgrounds. The
students will
be expected to put in at least 5 hours per week working on their
assigned project.
Each student will have their own problem but they will all be closely related.
Students will be strongly encouraged to work in groups at least part
of the time.
I have done this type of seminar before (with high school students
even) and find
that because the students will have large difference in computational skills,
the most efficient way to bring the weaker ones up is to pair them
with the stronger.
Each student will give a report on their findings (or lack thereof) to rest of
the group and will write a short description of their analytical
methods and results.
Grading: The course will be graded in the
following manner.
At the end of the quarter each student will write up a report on the work they
have done over the quarter. This paper will constitute 1/3 of the grade. On the
last day, each student will give a 20 minute oral presentation of their paper.
This will constitute 1/3 of the grade. The last 1/3 of the grade will be based
on participation and preparedness for the regular discussions during
the quarter.
About the
Instructor: