A genetic algorithm for simplifying the amino acid alphabet in bioinformatics applications

Matthew Palensky, Hesham H Ali

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Simplifying the representation of protein sequences have been receiving considerable attention in recent years since having a simplified representation will potentially allow for the ability to tackle difficult problems such as the prediction of protein interaction. A central problem in creating simplified amino acid alphabets is narrowing down the massive number of possible simplifications. Since considering all possible simplifications is intractable, effectively creating simplified alphabets is essential. Genetic algorithms have been effective in providing near-optimal solutions for similar combinatorial problems with large solution spaces. This makes them a good candidate for creating simplified alphabets. Simplified amino acid alphabets could uncover hidden relationships in protein sequences, and in turn provide a valuable first step in solving protein-related microbiological problems. Simplifying amino acid alphabets may potentially reduce the degree of complexity for several difficult problems such as protein prediction interaction and protein structure prediction.

Original languageEnglish (US)
Title of host publicationProceedings of the IASTED International Conference on Artificial Intelligence and Applications, AIA 2006
Pages19-25
Number of pages7
StatePublished - 2006
EventIASTED International Conference on Artificial Intelligence and Applications, AIA 2006 - Innsbruck
Duration: Feb 13 2006Feb 16 2006

Other

OtherIASTED International Conference on Artificial Intelligence and Applications, AIA 2006
CityInnsbruck
Period2/13/062/16/06

Fingerprint

Bioinformatics
Amino acids
Genetic algorithms
Proteins

Keywords

  • Amino acid alphabet
  • Bioinformatics
  • Genetic algorithms
  • Protein sequences

ASJC Scopus subject areas

  • Artificial Intelligence
  • Computer Science Applications
  • Software

Cite this

Palensky, M., & Ali, H. H. (2006). A genetic algorithm for simplifying the amino acid alphabet in bioinformatics applications. In Proceedings of the IASTED International Conference on Artificial Intelligence and Applications, AIA 2006 (pp. 19-25)

A genetic algorithm for simplifying the amino acid alphabet in bioinformatics applications. / Palensky, Matthew; Ali, Hesham H.

Proceedings of the IASTED International Conference on Artificial Intelligence and Applications, AIA 2006. 2006. p. 19-25.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Palensky, M & Ali, HH 2006, A genetic algorithm for simplifying the amino acid alphabet in bioinformatics applications. in Proceedings of the IASTED International Conference on Artificial Intelligence and Applications, AIA 2006. pp. 19-25, IASTED International Conference on Artificial Intelligence and Applications, AIA 2006, Innsbruck, 2/13/06.
Palensky M, Ali HH. A genetic algorithm for simplifying the amino acid alphabet in bioinformatics applications. In Proceedings of the IASTED International Conference on Artificial Intelligence and Applications, AIA 2006. 2006. p. 19-25
Palensky, Matthew ; Ali, Hesham H. / A genetic algorithm for simplifying the amino acid alphabet in bioinformatics applications. Proceedings of the IASTED International Conference on Artificial Intelligence and Applications, AIA 2006. 2006. pp. 19-25
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