Using Bioinformatics to Make the Bio-Math Connection

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Using Bioinformatics to Make the Bio-Math
Connection

• The Confessions of a Biology Teacher

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Math? In a Biology Classroom?
I know what you are thinking, and Ive just
written an algorithm that proves it is very
effective.
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• "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.).

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bioinformatics
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.
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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.

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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.

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Student Interface to the Biology Workbench (BSW)

• alternative interface to the Biology Workbench
  orientated towards interactive teaching and
  learning

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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

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Protein Tools

• May also do protein searchesNdjinn
• May look for similar proteinsBLASTP
• Protein tools are more reliable for looking at
  evolutionary relationships

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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

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Rooted Tree
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Unrooted Tree
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Graph Theory

• A connected graph without a cycle is a tree.

http//people.hofstra.edu/geotrans/eng/ch2en/meth2
en/ch2m1en.html
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Biology Uses

• Find compare DNA sequences
• Translate DNA into an amino acid sequence
• Find compare protein sequences
• Look at evolutionary relationships
• Draw trees

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Math Uses

• Alignments
• Matrixes
• Graphs
• Combinatorics

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• "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.)