Secrets’NSequences
Begin by Beading Bioinformatics
“Dr Toby” Horn
Toby M Horn, PhD thorn@ciw.edu
What we’ll do
• About Bioinformatics
• Model-building
• Connecting your model to real
sequence information
• Extensions and teaching strategies
Toby M Horn, PhD thorn@ciw.edu
We dance round in a ring
and suppose
But the Secret sits in the middle
and knows.
The Secret Sits by Robert Frost
Toby M Horn, PhD thorn@ciw.edu
bioinformatics is …
• the use of computer science, mathematics, and
information theory to model and analyze
biological systems.
• the collection, organization and analysis of
large amounts of biological data, using
networks of computers and databases.
• the use of computing tools to manage and
analyze genomic and molecular biological data.
Toby M Horn, PhD thorn@ciw.edu
So What?
Toby M Horn, PhD thorn@ciw.edu
Applications of Bioinformatics
• Understanding how our genomes work
• Tracing the pathway of emerging
diseases
• Developing modified strains of crops
with better quality and quantity of
protein, vitamin, oil
• And more
Toby M Horn, PhD thorn@ciw.edu
Model a DNA Sequence with
Color-Coded Nucleotides
A
C
G
T
Toby M Horn, PhD thorn@ciw.edu
Source of Beads
(and elastic findings)
QuickTime™ and a
decompressor
are needed to see this picture.
www.consumercrafts.c
om
(acrylic faceted beads,
8mm)
Toby M Horn, PhD thorn@ciw.edu
Toby M Horn, PhD thorn@ciw.edu
Toby M Horn, PhD thorn@ciw.edu
Mnemonics help us remember
So, we make color choices based on…
• Sounds
–Adenine-Red
–Guanine-Gold
–Cytosine-SkyBlue
• School Colors (Ballou/McKinley)
• Fashion
Toby M Horn, PhD thorn@ciw.edu
What You’ll Do
A. String 18 beads in a pattern (or not)
that YOU like
B. Enter the sequence in GenBank
C. Discover the secret of your sequence
Toby M Horn, PhD thorn@ciw.edu
Stringing Your Beads
You have a bracelet length of elastic.
1. Tie a double knot in one end, leaving about 3 cm.
2. Bead from the long end of the elastic.
3. Stretch the elastic just a little and tie a double-knot
on the free end close to the beads (should leave
about 3 cm or more).
4. Bead both ends through another bead. Double
knot the ends together. Cut the longer piece of
elastic.
Toby M Horn, PhD thorn@ciw.edu
Stringing Your Beads
1. Tie a double
knot in one end,
leaving about 3
cm.
2.
3.
4.
Bead from the long end of the elastic.
Stretch the elastic just a little and tie a double-knot
on the free end close to the beads (should leave
about 3 cm or more).
Bead both ends through another bead. Double knot
the ends together. Cut the longer piece of elastic.
Toby M Horn, PhD thorn@ciw.edu
Stringing Your Beads
1.
Tie a double knot in one end, laving about 3 cm.
2. Bead from the
long end of the
elastic.
3.
4.
Stretch the elastic just a little and tie a double-knot
on the free end close to the beads (should leave
about 3 cm or more).
Bead both ends through another bead. Double knot
the ends together. Cut the longer piece of elastic.
Toby M Horn, PhD thorn@ciw.edu
Stringing Your Beads
1.
2.
Tie a double knot in one end, leaving about 3 cm.
Bead from the long end of the elastic.
3. Stretch the elastic
just a little and tie a
double-knot on the
free end close to
the beads (should
leave about 3 cm
or more).
4.
Bead both ends through another bead. Double knot
the ends together. Cut the longer piece of elastic.
Toby M Horn, PhD thorn@ciw.edu
Stringing Your Beads
1.
2.
3.
Tie a double knot in one end, leaving about 3 cm.
Bead from the long end of the elastic.
Stretch the elastic just a little and tie a double-knot
on the free end close to the beads (should leave
about 3 cm or more).
4. Bead both ends
through another
bead. Double knot
the ends together.
Cut the longer
piece of elastic.
Toby M Horn, PhD thorn@ciw.edu
Write Your DNA Sequence with
Color-Coded Nucleotides
1
18
A
C
G
T
Toby M Horn, PhD thorn@ciw.edu
Visit GenBank
http://www.ncbi.
nlm.nih.gov
GenBank is celebrating its 25th
Anniversary in April!
Toby M Horn, PhD thorn@ciw.edu
BLAST is the section of GenBank
where you can search a sequence
Toby M Horn, PhD thorn@ciw.edu
Toby M Horn, PhD thorn@ciw.edu
Scroll down to
Basic BLAST
Toby M Horn, PhD thorn@ciw.edu
Type your sequence here
Toby M Horn, PhD thorn@ciw.edu
Toby M Horn, PhD thorn@ciw.edu
Toby M Horn, PhD thorn@ciw.edu
Toby M Horn, PhD thorn@ciw.edu
Be
Patient!
Toby M Horn, PhD thorn@ciw.edu
Confirms the number of nucleotides
you entered
Toby M Horn, PhD thorn@ciw.edu
Graphical comparisons
Toby M Horn, PhD thorn@ciw.edu
Hints About the Secret
Sequence are Revealed
Species, Location, more
Toby M Horn, PhD thorn@ciw.edu
Where is your sequence?
Toby M Horn, PhD thorn@ciw.edu
Maybe your
sequence
codes for
protein or
some other
known
function
Toby M Horn, PhD thorn@ciw.edu
The File Data
Toby M Horn, PhD thorn@ciw.edu
The
Sequence
Data
Toby M Horn, PhD thorn@ciw.edu
MORE
Secrets
in the
Sequenc
e
Toby M Horn, PhD thorn@ciw.edu
Resources
• National Center for Biotechnology Information
www.ncbi.nlm.nih.gov
• Sandra Porter - Geospiza
www.geospiza.com/education/
• DNA From the Beginning, CSHL
www.dnalc.org
• J-M Claverie & C Notredame Bioinformatics
for Dummies. Wiley. 2003.
Toby M Horn, PhD thorn@ciw.edu
Crafts
Search: beads plastic facet
Beads (facet, 8 mm) and fine elastic cord
– www.consumercrafts.com (Consumer
Crafts)
– Michaels, WalMart, BenFranklin, Jo-Ann for
small quantities
– www.ssww.com (S&S Wholesale for pony
beads and pop-beads)
Toby M Horn, PhD thorn@ciw.edu
http://www.dcbiotech.org
Check out
Teaching Resources
Toby M Horn, PhD thorn@ciw.edu
Get your kids to
dig deeper, by
starting here!
Toby M Horn, PhD thorn@ciw.edu