Lesson Plan - Bioinformatics Activity Bank

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Oct 1, 2013 (3 years and 8 months ago)

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Computation and DNA Sequencing
:
Lesson Plan


Overview

This activity introduces

students to the computation involved in

reassembling sequenced DNA to
reconstruct the original gene. The activity enhances a reading and activity from Professor Ann Condon of
the University of British Columbia that discusses the genetics and programming concepts. This extends
those activitities by including some actual Python programming exercises and examples.


SWBAT:

Describe how DNA fragments are assembled into gene sequenc
es

Use Python string and itertools capabilities to implement a recombination algorithm




R
eview of the basic structure of DNA

by
read
ing

section 6.1 of “Digital DNA” article as homework,
discuss exercises 6.1.1 and 6.1.2 in class.



Read: section 6.2.1 and 6.
2.2 of
Professor Condon’s
“Digital DNA” article

http://www.cs.ubc.ca/~condon/cpsc101/notes/digital
-
dna.pdf
.
Professor Condon’s slides are
available at

http://www.cs.ubc.ca/~condon/cpsc101/lectures/lec29.pdf

and
http://www.cs.ubc.ca/~condon/cpsc101/lectures/lec30.pdf



H
ave students do exercise
s 6.2.1 and 6.2.2

from reading.



At this point they have sufficient background to attempt to write a brute
-
force program to
recombine fragments and find the shortest solution. This is a challenging but not impossible
pro
blem for high school students.



Progr
am

should

be tested with the accompanying data files.
S
tudents
will
note how the time to
run the program grows as
n!
, where
n

is the number of segments to be combined.

Discuss why this
is the case, and extrapolate to how long the program would take to f
ind the shortest solution for
reassembling 20 segments, or 100 segments.


Materials



Python programming environment, test data files
.


Assessment



Class exercises from reading, p
rogramming assignment


Resources



http://www.ornl.gov/sci/techresources/Human_Genome/faq/seqfacts.shtml
: background
information on Human Genome sequencing, in FAQ format.



http://www.dnalc.org/view/15477
-
The
-
public
-
Human
-
Genome
-
Project
-
mapping
-
the
-
genome
-
sequencing
-
and
-
reassembly
-
3D
-
animation
-
.html

Animation showing sequencing and reassembly



http://bioteach.ubc.ca/Bioinformatics/interviews/
:

“An Interview with Two Bioinformaticians:
Bioinformatics from the Computer Science and Biology Perspectives”