Creation of Motifs that Detect the D–E–A–D Box Family of Proteins and the Manganese Superoxide Dismutase Family
(A Human-Competitive Result Produced by Genetic Programming)
Genetic programming evolved motifs that detect the D–E–A–D box family of proteins and the manganese superoxide dismutase family as described in section 59.8 of Genetic Programming III: Darwinian Invention and Problem Solving (Koza, Bennett, Andre, and Keane 1999).
The genetically evolved motif for the D–E–A–D box family of proteins is
[IV]-[lim]-D-E-[AI]-D-[rnek]-[lim]-[lim]-[limeqdnrsk]
PROSITE
is a database of biologically meaningful patterns found in protein sequences
(Bairoch and Bucher 1994). When tested against the SWISS-PROT database of
proteins, the two evolved consensus motifs detect the two families as well as,
or slightly better than, the human-written motifs placed in the PROSITE
database by an international committee of human experts on molecular biology.
Referring to the eight criteria in chapter 1 of Genetic Programming III: Darwinian Invention and Problem Solving (Koza, Bennett, Andre, and Keane 1999) for establishing that an automatically created result is competitive with a human-produced result, the automatic synthesis of a motifs that detect the D–E–A–D box family of proteins and the manganese superoxide dismutase family satisfies the following criterion:
(C) The
result is equal to or better than a result that was placed into a database or
archive of results maintained by an internationally recognized panel of
scientific experts.
Bairoch,
Amos; and Boeckmann, B. 1991. The SWISS-PROT protein sequence data bank:
Current status. Nucleic Acids Research 22(17):3578-3580.
Koza, John R., Bennett III, Forrest H, Andre, David, and Keane, Martin A. 1999a. Genetic Programming III: Darwinian Invention and Problem Solving. San Francisco, CA: Morgan Kaufmann.
· The home page of Genetic Programming Inc. at www.genetic-programming.com.
· For information about the field of genetic programming and the field of genetic and evolutionary computation, visit www.genetic-programming.org
· The home page of John R. Koza at Genetic Programming Inc. (including online versions of most published papers) and the home page of John R. Koza at Stanford University
· For information about John Koza’s course on genetic algorithms and genetic programming at Stanford University
· Information about the 1992
book Genetic
Programming: On the Programming of Computers by Means of Natural Selection,
the 1994 book Genetic
Programming II: Automatic Discovery of Reusable Programs, the 1999
book Genetic
Programming III: Darwinian Invention and Problem Solving, and the
2003 book Genetic
Programming IV: Routine
Human-Competitive Machine Intelligence. Click here to read chapter 1 of Genetic
Programming IV book in PDF format.
· 3,440
published papers on genetic programming (as of November 28, 2003) in a
searchable bibliography (with many on-line versions of papers) by over 880
authors maintained by William Langdon’s and Steven M. Gustafson.
· For information on the Genetic Programming and Evolvable Machines journal published by Kluwer Academic Publishers
· For information on the Genetic Programming book series from Kluwer Academic Publishers, see the Call For Book Proposals
· For information about the annual Genetic and Evolutionary Computation (GECCO) conference (which includes the annual GP conference) to be held on June 26–30, 2004 (Saturday – Wednesday) in Seattle and its sponsoring organization, the International Society for Genetic and Evolutionary Computation (ISGEC). For information about the annual Euro-Genetic-Programming Conference to be held on April 5-7, 2004 (Monday – Wednesday) at the University of Coimbra in Coimbra Portugal. For information about the 2003 and 2004 Genetic Programming Theory and Practice (GPTP) workshops held at the University of Michigan in Ann Arbor. For information about Asia-Pacific Workshop on Genetic Programming (ASPGP03) held in Canberra, Australia on December 8, 2003. For information about the annual NASA/DoD Conference on Evolvable Hardware Conference (EH) to be held on June 24-26 (Thursday-Saturday), 2004 in Seattle.
Last updated on December 28, 2003