Hostname: page-component-78c5997874-mlc7c Total loading time: 0 Render date: 2024-11-13T06:15:04.706Z Has data issue: false hasContentIssue false
  • English
  • Français

Genetic and Tabu search algorithmsfor peptide assembly problem

Published online by Cambridge University Press:  27 April 2010

Jacek Błażewicz ,
Marcin Borowski ,
Piotr Formanowicz  and
Tomasz Głowacki
Jacek Błażewicz
Affiliation:
Institute of Computing Science, Poznań University of Technology, Piotrowo 2, 60-965 Poznań, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; J. Błażewicz: jblazewicz@cs.put.poznan.pl
Marcin Borowski
Affiliation:
Institute of Computing Science, Poznań University of Technology, Piotrowo 2, 60-965 Poznań, Poland.
Piotr Formanowicz
Affiliation:
Institute of Computing Science, Poznań University of Technology, Piotrowo 2, 60-965 Poznań, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; J. Błażewicz: jblazewicz@cs.put.poznan.pl
Tomasz Głowacki
Affiliation:
Institute of Computing Science, Poznań University of Technology, Piotrowo 2, 60-965 Poznań, Poland.
Get access

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.

Keywords

Peptide sequencingcombinatorial optimization problemgenetic algorithmtabu search algorithm
Type
Research Article
Information
RAIRO - Operations Research , Volume 44 , Issue 2 , April 2010 , pp. 153 - 166
Copyright
© EDP Sciences, ROADEF, SMAI, 2010

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Błażewicz, J., Borowski, M., Formanowicz, P. and Głowacki, T., On graph theoretical models for peptide sequence assembly. Foundations of Computing and Decision Sciences 30 (2005) 183–191.
Błażewicz, J., Borowski, M., Formanowicz, P. and Stobiecki, M., Tabu Search Method for Determining Sequences of Amino Acids in Long Polypeptides. Lect. Notes Comput. Sci. 3449 (2005) 22–32. CrossRef
Błażewicz, J. and Kasprzak, M., Combinatorial optimization in DNA mapping – a computational thread of the Simplified Partial Digest Problem. RAIRO - Oper. Res. 39 (2005) 227–241. CrossRef
Błażewicz, J., Formanowicz, P. and Kasprzak, M., Selected combinatorial problems of computational biology. Eur. J. Oper. Res. 161 (2005) 585–597. CrossRef
P. Formanowicz, Selected Combinatorial Aspects of Biological Sequence Analysis, Poznań, Publishing House of Poznań University of Technology (2005).
J.K. Gallant, The complexity of the overlap method for sequencing biopolymers, J. Theo. Biol. 101 (1983) 1–17.
Glover, F., Tabu Search, Part I. ORSA Journal on Computing 1 (1989) 190–206. CrossRef
Glover, F., Tabu Search, Part II. ORSA Journal on Computing 1 (1990) 4–32. CrossRef
Needleman, S.B and Wunsch, C.D., A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48 (1970) 443–453. CrossRef
P.A. Pevzner, Comput. molecular biology. An algorithmic approach. Cambridge, Massachusetts, The MIT Press (2000).
J.C. Setubal and J. Meidanis, Introduction to computational molecular biology. Boston, PWS Publishing Co. (1996).
L. Stryer, Biochemistry, 4th edition. New York, W.H. Freeman and Company (1995).
M.S. Waterman, Introduction to computational biology, London, Chapman & Hall (1995).