blast genomics data in the public domain stacy lavin igsp center for genome ethics, law & policy
Post on 20-Dec-2015
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TRANSCRIPT
Agenda
• Historical background of bioinformatics
• The beginnings of BLAST
• GenBank
• BLAST and IP
• Interviews with BLAST creators
Why BLAST?
Journal Citation Trends of Altschul et. al. (1990)
Patent Citation Trends of (USPTO) OREF/ BLAST and Altschul
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19901991199219931994
199519961997199819992000
20012002200320042005
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
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….
“Basic Local Alignment Tool” J Mol Biol (1990)
Stephen Altschul, Warren Gish, Webb Miller, Gene Myers, David Lipman
Margaret O. DayhoffDavid J.Lipman
Collaboration
LipmanDirector
NCBI
FAST 1985
Eugene Myers
Arizona University
Idea forrigorous algorithm
Warren Gish
NCBI
Wrote revised code
Webb Miller
Penn State University
Wrote first code
Stephen Altschul
NCBI
StatisticsWrote the paper
“But it wasn’t necessarily going to turn out that way.”
~Altschul, personal correspondence in July 2005
Webb Miller• HGP conscript
• Not with public funds
• No licensing at PSU– GALA– New analysis
methods
BLAST: Problems for IP
• Speed matters
• Tools like BLAST aren’t usually substitutive
• More coveted than analysis tools are the data themselves