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BLAST Genomics Data in the Public Domain

BLAST Genomics Data in the Public Domain. Stacy Lavin IGSP Center for Genome Ethics, Law & Policy. Agenda. Historical background of bioinformatics The beginnings of BLAST GenBank BLAST and IP Interviews with BLAST creators. Why BLAST?.

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BLAST Genomics Data in the Public Domain

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  1. BLAST Genomics Data in the Public Domain Stacy Lavin IGSP Center for Genome Ethics, Law & Policy

  2. Agenda • Historical background of bioinformatics • The beginnings of BLAST • GenBank • BLAST and IP • Interviews with BLAST creators

  3. Why BLAST? Patent Citation Trends of (USPTO) OREF/ BLASTandAltschul Journal Citation Trends of Altschul et. al. (1990)

  4. Background Sequence Alignment • Lewis Carroll 1879 Vanity Fair • Heads --> “heal” “teal” “tail” “tell” --> tails • Single letter substitutions • R.W. Hamming 1950 Bell System Tech J • Ulam-Smith 1972 Ann Review of Biophysics and Biomathematics

  5. Computational and Theoretical Frontiers of Biology Zuckerkandl and Pauling (1964) Molecules as Documents of Evolutionary History Dayhoff (1964) Computer Aids to Protein Sequence Comparison Sanger (1956) The Structure of Insulin Sanger and Coulson (1975) A Rapid Method for Determining Sequences in DNA….

  6. “Basic Local Alignment Tool” J Mol Biol (1990) StephenAltschul, Warren Gish, Webb Miller, Gene Myers, David Lipman David J.Lipman MargaretO. Dayhoff

  7. Collaboration Warren Gish NCBI Wrote revised code Eugene Myers Arizona University Idea for rigorous algorithm Webb Miller Penn State University Wrote first code Stephen Altschul NCBI Statistics Wrote the paper

  8. 1979 – 1992: Los Alamos 1992 forward: NCBI GenBank

  9. “But it wasn’t necessarily going to turn out that way.” ~Altschul, personal correspondence in July 2005

  10. Patenting DNA Data Analysis Algorithms

  11. Stephen Altschul • Infrastructure • Incentive • Investment

  12. Webb Miller • HGP conscript • Not with public funds • No licensing at PSU • GALA • New analysis methods

  13. BLAST: Problems for IP • Speed matters • Tools like BLAST aren’t usually substitutive • More coveted than analysis tools are the data themselves

  14. Questions?

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