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Secrets’NSequences

Secrets’NSequences. Begin by Beading Bioinformatics “Dr Toby” Horn. What we’ll do. About Bioinformatics Model-building Connecting your model to real sequence information Extensions and teaching strategies. We dance round in a ring and suppose But the Secret sits in the middle and knows.

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Secrets’NSequences

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  1. Secrets’NSequences Begin by Beading Bioinformatics “Dr Toby” Horn Toby M Horn, PhD thorn@ciw.edu

  2. 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

  3. We dance round in a ring and suppose But the Secretsits in the middle and knows. The Secret Sits by Robert Frost Toby M Horn, PhD thorn@ciw.edu

  4. 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

  5. So What? Toby M Horn, PhD thorn@ciw.edu

  6. 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

  7. Model a DNA Sequence with Color-Coded Nucleotides A C T G Toby M Horn, PhD thorn@ciw.edu

  8. Source of Beads (and elastic findings) www.consumercrafts.com (acrylic faceted beads, 8mm) Toby M Horn, PhD thorn@ciw.edu

  9. Toby M Horn, PhD thorn@ciw.edu

  10. Toby M Horn, PhD thorn@ciw.edu

  11. Mnemonicshelp us rememberSo, 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

  12. What You’ll Do • String 18 beads in a pattern (or not) that YOU like • Enter the sequence in GenBank • Discover the secret of your sequence Toby M Horn, PhD thorn@ciw.edu

  13. Stringing Your Beads You have a bracelet length of elastic. • 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). • Bead both ends through another bead. Double knot the ends together. Cut the longer piece of elastic. Toby M Horn, PhD thorn@ciw.edu

  14. Stringing Your Beads • 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). • Bead both ends through another bead. Double knot the ends together. Cut the longer piece of elastic. Toby M Horn, PhD thorn@ciw.edu

  15. Stringing Your Beads • Tie a double knot in one end, laving 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). • Bead both ends through another bead. Double knot the ends together. Cut the longer piece of elastic. Toby M Horn, PhD thorn@ciw.edu

  16. Stringing Your Beads • 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). • Bead both ends through another bead. Double knot the ends together. Cut the longer piece of elastic. Toby M Horn, PhD thorn@ciw.edu

  17. Stringing Your Beads • 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). • Bead both ends through another bead. Double knot the ends together. Cut the longer piece of elastic. Toby M Horn, PhD thorn@ciw.edu

  18. Write Your DNA Sequence with Color-Coded Nucleotides A 1 18 C T G Toby M Horn, PhD thorn@ciw.edu

  19. Visit GenBank http://www.ncbi. nlm.nih.gov GenBank is celebrating its 25th Anniversary in April! Toby M Horn, PhD thorn@ciw.edu

  20. BLAST is the section of GenBank where you can search a sequence Toby M Horn, PhD thorn@ciw.edu

  21. Toby M Horn, PhD thorn@ciw.edu

  22. Scroll down to Basic BLAST Toby M Horn, PhD thorn@ciw.edu

  23. Type your sequence here Toby M Horn, PhD thorn@ciw.edu

  24. Toby M Horn, PhD thorn@ciw.edu

  25. Toby M Horn, PhD thorn@ciw.edu

  26. Toby M Horn, PhD thorn@ciw.edu

  27. Be Patient! Toby M Horn, PhD thorn@ciw.edu

  28. Confirms the number of nucleotides you entered Toby M Horn, PhD thorn@ciw.edu

  29. Graphical comparisons Toby M Horn, PhD thorn@ciw.edu

  30. Hints About the SecretSequence are Revealed Species, Location, more Toby M Horn, PhD thorn@ciw.edu

  31. Where is your sequence? Toby M Horn, PhD thorn@ciw.edu

  32. Maybe your sequence codes for protein or some other known function Toby M Horn, PhD thorn@ciw.edu

  33. The File Data Toby M Horn, PhD thorn@ciw.edu

  34. The Sequence Data Toby M Horn, PhD thorn@ciw.edu

  35. MORE Secrets in the Sequence Toby M Horn, PhD thorn@ciw.edu

  36. 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

  37. 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

  38. http://www.dcbiotech.orgCheck out Teaching Resources Toby M Horn, PhD thorn@ciw.edu

  39. Get your kids to dig deeper, by starting here! Toby M Horn, PhD thorn@ciw.edu

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