Genetic and Tabu search algorithms for peptide assembly problem

Jacek Błażewicz; Marcin Borowski; Piotr Formanowicz; Tomasz Głowacki

RAIRO - Operations Research (2010)

  • Volume: 44, Issue: 2, page 153-166
  • ISSN: 0399-0559

Abstract

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Determining amino acid sequences of protein molecules is one of the most important issues in molecular biology. These sequences determine protein structure and functionality. Unfortunately, direct biochemical methods for reading amino acid sequences can be used for reading short sequences only. This is the reason, which makes peptide assembly algorithms an important complement of these methods. In this paper, a genetic algorithm solving the problem of short amino acid sequence assembly is presented. The algorithm has been tested in computational experiment and compared with an existing tabu search method for the same problem. The results clearly show that the genetic algorithm outperformed the tabu search approach.

How to cite

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Błażewicz, Jacek, et al. "Genetic and Tabu search algorithms for peptide assembly problem." RAIRO - Operations Research 44.2 (2010): 153-166. <http://eudml.org/doc/250837>.

@article{Błażewicz2010,
abstract = { Determining amino acid sequences of protein molecules is one of the most important issues in molecular biology. These sequences determine protein structure and functionality. Unfortunately, direct biochemical methods for reading amino acid sequences can be used for reading short sequences only. This is the reason, which makes peptide assembly algorithms an important complement of these methods. In this paper, a genetic algorithm solving the problem of short amino acid sequence assembly is presented. The algorithm has been tested in computational experiment and compared with an existing tabu search method for the same problem. The results clearly show that the genetic algorithm outperformed the tabu search approach. },
author = {Błażewicz, Jacek, Borowski, Marcin, Formanowicz, Piotr, Głowacki, Tomasz},
journal = {RAIRO - Operations Research},
keywords = {Peptide sequencing; combinatorial optimization problem; genetic algorithm; tabu search algorithm; peptide sequencing},
language = {eng},
month = {4},
number = {2},
pages = {153-166},
publisher = {EDP Sciences},
title = {Genetic and Tabu search algorithms for peptide assembly problem},
url = {http://eudml.org/doc/250837},
volume = {44},
year = {2010},
}

TY - JOUR
AU - Błażewicz, Jacek
AU - Borowski, Marcin
AU - Formanowicz, Piotr
AU - Głowacki, Tomasz
TI - Genetic and Tabu search algorithms for peptide assembly problem
JO - RAIRO - Operations Research
DA - 2010/4//
PB - EDP Sciences
VL - 44
IS - 2
SP - 153
EP - 166
AB - Determining amino acid sequences of protein molecules is one of the most important issues in molecular biology. These sequences determine protein structure and functionality. Unfortunately, direct biochemical methods for reading amino acid sequences can be used for reading short sequences only. This is the reason, which makes peptide assembly algorithms an important complement of these methods. In this paper, a genetic algorithm solving the problem of short amino acid sequence assembly is presented. The algorithm has been tested in computational experiment and compared with an existing tabu search method for the same problem. The results clearly show that the genetic algorithm outperformed the tabu search approach.
LA - eng
KW - Peptide sequencing; combinatorial optimization problem; genetic algorithm; tabu search algorithm; peptide sequencing
UR - http://eudml.org/doc/250837
ER -

References

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  1. J. Błażewicz, M. Borowski, P. Formanowicz and T. Głowacki, On graph theoretical models for peptide sequence assembly. Foundations of Computing and Decision Sciences30 (2005) 183–191.  
  2. J. Błażewicz, M. Borowski, P. Formanowicz and M. Stobiecki, Tabu Search Method for Determining Sequences of Amino Acids in Long Polypeptides. Lect. Notes Comput. Sci.3449 (2005) 22–32.  
  3. J. Błażewicz and M. Kasprzak, Combinatorial optimization in DNA mapping – a computational thread of the Simplified Partial Digest Problem. RAIRO - Oper. Res.39 (2005) 227–241.  
  4. J. Błażewicz, P. Formanowicz and M. Kasprzak, Selected combinatorial problems of computational biology. Eur. J. Oper. Res.161 (2005) 585–597.  
  5. P. Formanowicz, Selected Combinatorial Aspects of Biological Sequence Analysis, Poznań, Publishing House of Poznań University of Technology (2005).  
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  7. F. Glover, Tabu Search, Part I. ORSA Journal on Computing1 (1989) 190–206.  
  8. F. Glover, Tabu Search, Part II. ORSA Journal on Computing1 (1990) 4–32.  
  9. S.B Needleman and C.D. Wunsch, A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol.48 (1970) 443–453.  
  10. P.A. Pevzner, Comput. molecular biology. An algorithmic approach. Cambridge, Massachusetts, The MIT Press (2000).  
  11. J.C. Setubal and J. Meidanis, Introduction to computational molecular biology. Boston, PWS Publishing Co. (1996).  
  12. L. Stryer, Biochemistry, 4th edition. New York, W.H. Freeman and Company (1995).  
  13. M.S. Waterman, Introduction to computational biology, London, Chapman & Hall (1995).  

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