Dinosaur bioinformatics
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Introductory lesson in sequence based bioinformatics for a local high school
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Dinosaur bioinformatics
- 1. DINOINFORMATICS Matt Vaughn, Director of Life Sciences Computing, Texas Advanced Computing Center
- 2. BIOINFORMATICS IS THE INTERSECTION OF COMPUTER SCIENCE AND BIOLOGY
- 3. By developing techniques for analyzing sequence data and structures, we can attempt to understand the basis of life
- 4. DNA SEQUENCING COSTS HAVE DECREASED FROM $1B/GENOME IN 2000 TO $500 in 2015
- 5. CHEAP DNA SEQUENCING HAS ALLOWED PEOPLE TO START ASKING REVOLUTIONARY QUESTIONS
- 6. WHERE DID MY ANCESTORS LIVE?
- 7. WHY DO LEAVES CHANGE COLOR IN THE FALL?
- 8. WHAT DOES THE BIRD FAMILY TREE LOOK LIKE?
- 9. AND ARE THEY REALLY RELATED TO DINOSAURS???
- 10. FULL GENOME SEQUENCING 45 BIRD GENOMES PLUS ANOLE, ALLIGATOR, SEA TURTLE LOOK AT EVERYTHING NOT JUST PROTEINS, SPECIFIC GENES, OR TRAITS
- 11. DATA TSUNAMI
- 12. 13,533 species 13,537 species
- 13. IN THE BIRD GENOMES DATA SET THERE ARE MORE POSSIBLE TREES THAN ATOMS IN THE UNIVERSE A) WRITE SMART ALGORITHMS
- 14. B) BRING ON THE HEAVY METAL COMPUTERS BIGGER THAN A 747 ENOUGH DISK TO HOLD 16000 BLU-RAYS INTERNET 1000X FASTER THAN HOME
- 15. OBVIOUS EXPLOSION AT 65MYA MOST BIRD FAMILIES WERE ESTABLISHED BY 50MYA BIRDS OF PREY ARE NOT MONOPHYLETIC OSTRICHES, CHICKENS, DUCKS ARE FOSSIL LINEAGES
- 16. PROTEOMICS IS SYSTEMATIC ANALYSIS OF PEPTIDE FRAGMENTS - WHAT ARE THE PROTEINS IN A GIVEN SAMPLE?
- 17. RESULT – STRINGS OF AMINO ACID SEQUENCES GETGPAGPAGPPGPAGAR
- 20. HADROSAUR COLLAGEN MATCHES THE FOSSIL BIRD LINEAGES – THERE IS OF COURSE A SMALL POSSIBILITY THAT THIS IS BY CHANCE, RIGHT? Gallus (Chicken) Meleagris (Turkey) Tinamus (Tinamou) Struthio (Ostrich)
- 22. WANT TO DO YOUR OWN PALEOINFORMATICS? EVERYTHING YOU NEED IS AT NCBI - TRY SEARCHING FOR TYRANNOSAURUS, MAMMOTH, OR NEANDERTHAL!
- 23. DISCUSSION AND QUESTION TIME!
Editor's Notes
- Important problems, interesting topics, great need for innovative and efficient solutions
- Break up genome into little bits Determine sequence of each Stitch together $1B 5 years $500.00 24 hours
- 48 GENOMES 100 BILLION BASES 25 BILLION BYTES 250 MILLION PAGES
- THIS KIND OF OVERWHELMING ABUNDANCE OF DATA IS OFTEN CALLED A DATA TSUNAMI MASSIVE CHALLENGE TO STORE, ORGANIZE, ANALYZE
- Basic phylogeny, parsimony, etc… As trees have more species and characters, search space to find optimal tree grows exponentially
- Be EFFICIENT AND SMART in your code But sometimes that’s not enough. Problem is too big for your local computer.
- DIVIDE AND CONQUER. But you have to have enough troops.
- Birds of prey are not monophyletic –ancestor was an apex predator Ostriches, Chickens, Ducks are really primitive lineages
- Go through the BLAST report, first pass…