A genetic programming method for protein motif discovery and protein classification
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- @Article{journals/soco/TsunodaFL11,
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author = "Denise Fukumi Tsunoda and Alex Alves Freitas and
Heitor Silverio Lopes",
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title = "A genetic programming method for protein motif
discovery and protein classification",
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journal = "Soft Computing - A Fusion of Foundations,
Methodologies and Applications",
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year = "2011",
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volume = "15",
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number = "10",
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pages = "1897--1908",
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publisher = "Springer",
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keywords = "genetic algorithms, genetic programming, evolutionary
algorithms, data mining, proteins patterns discovery",
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ISSN = "1432-7643",
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DOI = "doi:10.1007/s00500-010-0624-9",
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size = "12 pages",
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abstract = "Proteins can be grouped into families according to
some features such as hydrophobicity, composition or
structure, aiming to establish common biological
functions. This paper presents MAHATMA memetic
algorithm based highly adapted tool for motif
ascertainment-a system that was conceived to discover
features (particular sequences of amino acids, or
motifs) that occur very often in proteins of a given
family but rarely occur in proteins of other families.
These features can be used for the classification of
unknown proteins, that is, to predict their function by
their primary structure. Experiments were done with a
set of enzymes extracted from the Protein Data Bank.
The heuristic method used was based on genetic
programming using operators specially tailored for the
target problem. The final performance was measured
using sensitivity, specificity and hit rate. The best
results obtained for the enzyme dataset suggest that
the proposed evolutionary computation method is
effective in finding predictive features (motifs) for
protein classification.",
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notes = "PDB, MAHATMA From the issue entitled Special Issue on
Intelligent Systems, Design and Applications (ISDA
2009)",
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affiliation = "Federal University of Parana, Av. Prefeito Lothario
Meissner, 632, Room 38, Curitiba, PR, Brazil",
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bibdate = "2011-09-14",
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bibsource = "DBLP,
http://dblp.uni-trier.de/db/journals/soco/soco15.html#TsunodaFL11",
- }
Genetic Programming entries for
Denise Fukumi Tsunoda
Alex Alves Freitas
Heitor Silverio Lopes
Citations