A genetic programming method for protein motif discovery and protein classification

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@Article{journals/soco/TsunodaFL11,

• author = "Denise Fukumi Tsunoda and Alex Alves Freitas and Heitor Silverio Lopes",
• title = "A genetic programming method for protein motif discovery and protein classification",
• journal = "Soft Computing - A Fusion of Foundations, Methodologies and Applications",
• year = "2011",
• volume = "15",
• number = "10",
• pages = "1897--1908",
• publisher = "Springer",
• keywords = "genetic algorithms, genetic programming, evolutionary algorithms, data mining, proteins patterns discovery",
• ISSN = "1432-7643",
• DOI = "doi:10.1007/s00500-010-0624-9",
• size = "12 pages",
• 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.",
• notes = "PDB, MAHATMA From the issue entitled Special Issue on Intelligent Systems, Design and Applications (ISDA 2009)",
• affiliation = "Federal University of Parana, Av. Prefeito Lothario Meissner, 632, Room 38, Curitiba, PR, Brazil",
• bibdate = "2011-09-14",
• 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

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