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Genetic and Tabu search algorithms for 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.
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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

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References

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