Using Bioinformatics to Make the Bio-Math 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·icsThe 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 web-

based 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.)