BLAST Genomics Data in the

Public Domain

Stacy LavinIGSP 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?

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

GenBank

• 1979 – 1992:

Los Alamos

• 1992 forward:

NCBI

“But it wasn’t necessarily going to turn out that way.”

~Altschul, personal correspondence in July 2005

Patenting DNA Data Analysis Algorithms

Stephen Altschul

• Infrastructure

• Incentive

• Investment

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

Questions?