Using Bioinformatics
to Make the BioMath Connection
The Confessions of a Biology
Teacher
Math? In a
Biology
Classroom?
I know what you
are thinking, and
I’ve just written
an algorithm that
proves it is very
effective.
"Complex assemblies of interacting proteins carry
out most of the interesting jobs in a cell, such as
metabolism, DNA synthesis, movement and
information processing. These physiological
properties play out as a subtle molecular dance,
choreographed by underlying regulatory
networks. To understand this dance, a new
breed of theoretical molecular biologists
reproduces these networks in computers and in
the mathematical language of dynamical
systems." (From "Network dynamics and cell
physiology", by Tyson, Chen, and Novak, Nature
Reviews in Molecular Cell Biology, 2001.).
bi·o·in·for·mat·ics
The use of mathematical and informational
techniques to solve biological problems by
using computer programs. One of the main
applications of bioinformatics is the data
mining in and analysis of the data gathered in
genome projects. Other applications are
amino acid and nucleic acid sequence
alignment, protein structure prediction, and
virtual evolution.
Biology Student Workbench



revolutionary webbased tool
allows biologists to
search protein and
DNA databases around
the world
integrated with access
to a wide variety of
analysis and modeling
tools, all within a point
and click interface.
Outcomes and Observations
•Integration of bioinformatics into the
high school classroom using inquiry
methods was successful.
•Students were able to use the tools to
generate real data, but more
importantly were able to apply these
applications and independently
problem solve.
•Students showed a greatly increased ability to make connections
between units of study: protein structure, protein function,
nucleic acids, genetics, genetic disease, and evolution.
Student Interface to the Biology
Workbench (BSW)
alternative interface to the Biology
Workbench orientated towards interactive
teaching and learning
BLASTN & MATH

Aligns the original strand with other strands
AGCGT
-CAGT
AGCGT
C-AGT
AGCGT
CA-GT
AGCGT
CAG-T
AGCGT
CAGT-
AGCG-T
C--AGT
-AGCGT
C--AGT
AGC-GT
--CAGT
Numerous possibilities exist, but which alignment is the best?
A scoring criterion must be devised to evaluate the quality of an alignment.
For example, the alignment may be scored based on the following criterion:
+2 for each alignment of matched letters
-1 for each alignment of mismatched letters
-2 for each alignment of a letter with a gap
Protein Tools
May also do protein searches…Ndjinn
 May look for similar proteins…BLASTP
 Protein tools are more reliable for looking
at evolutionary relationships

Clustal Distance Matrix
(1)
(2) (3)
(4)
(5) (6)
(1) 0.000 0.000 0.007 0.000 0.021 0.028
(2) 0.000 0.000 0.007 0.000 0.021 0.028
(3) 0.007 0.007 0.000 0.007 0.028 0.035
(4) 0.000 0.000 0.007 0.000 0.021 0.028
(5) 0.021 0.021 0.028 0.021 0.000 0.028
(6) 0.028 0.028 0.035 0.028 0.028 0.000
Rooted
Tree
Unrooted
Tree
Graph Theory

A connected graph without a cycle is a
tree.
http://people.hofstra.edu/geotrans/eng/ch2en/meth2en/ch2m1en.html
Biology Uses
Find & compare DNA sequences
 Translate DNA into an amino acid
sequence
 Find & compare protein sequences
 Look at evolutionary relationships
 Draw trees

Math Uses
Alignments
 Matrixes
 Graphs
 Combinatorics

"The slippery gooiness of biology is a
consequence of its incredible complexity,
consisting as it does of complex systems
based upon chemistry. And chemistry
obeys the rules of physics, which exists
because of, and is consequently best
described by, mathematics." (From the
Mathematics in Biology page at Brandeis.)