An enhanced genetic algorithm for DNA sequencing by hybridization with positive and negative errors

Thang N. Bui; Waleed A. Youssef

doi:10.1007/978-3-540-24855-2_104

An enhanced genetic algorithm for DNA sequencing by hybridization with positive and negative errors

Thang N. Bui, Waleed A. Youssef

School of Science, Engineering & Technology (Harrisburg)

Research output: Chapter in Book/Report/Conference proceeding › Chapter

9 Scopus citations

Abstract

This paper describes a genetic algorithm for the DNA sequencing problem. The algorithm allows the input spectrum to contain both positive and negative errors as could be expected from a hybridization experiment. The main features of the algorithm include a preprocessing step that reduces the size of the input spectrum and an efficient local optimization. In experimental tests, the algorithm performed very well against existing algorithms. The algorithm also performed very well on a large data set generated in this paper from real genomes data.

Original language	English (US)
Title of host publication	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Editors	Riccardo Poli, Owen Holland, Wolfgang Banzhaf, Hans-Georg Beyer, Edmund Burke, Paul Darwen, Dipankar Dasgupta, Dario Floreano, James Foster, Mark Harman, Pier Luca Lanzi, Lee Spector, Andrea G. B. Tettamanzi, Dirk Thierens, Andrew M. Tyrrell
Publisher	Springer Verlag
Pages	908-919
Number of pages	12
ISBN (Print)	3540223436
DOIs	https://doi.org/10.1007/978-3-540-24855-2_104
State	Published - 2004

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	3103
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

All Science Journal Classification (ASJC) codes

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-540-24855-2_104

Cite this

Bui, T. N., & Youssef, W. A. (2004). An enhanced genetic algorithm for DNA sequencing by hybridization with positive and negative errors. In R. Poli, O. Holland, W. Banzhaf, H.-G. Beyer, E. Burke, P. Darwen, D. Dasgupta, D. Floreano, J. Foster, M. Harman, P. L. Lanzi, L. Spector, A. G. B. Tettamanzi, D. Thierens, & A. M. Tyrrell (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (pp. 908-919). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3103). Springer Verlag. https://doi.org/10.1007/978-3-540-24855-2_104

Bui, Thang N. ; Youssef, Waleed A. / An enhanced genetic algorithm for DNA sequencing by hybridization with positive and negative errors. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). editor / Riccardo Poli ; Owen Holland ; Wolfgang Banzhaf ; Hans-Georg Beyer ; Edmund Burke ; Paul Darwen ; Dipankar Dasgupta ; Dario Floreano ; James Foster ; Mark Harman ; Pier Luca Lanzi ; Lee Spector ; Andrea G. B. Tettamanzi ; Dirk Thierens ; Andrew M. Tyrrell. Springer Verlag, 2004. pp. 908-919 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

@inbook{a6fdc1377429430a9896e29c9872cd30,

title = "An enhanced genetic algorithm for DNA sequencing by hybridization with positive and negative errors",

abstract = "This paper describes a genetic algorithm for the DNA sequencing problem. The algorithm allows the input spectrum to contain both positive and negative errors as could be expected from a hybridization experiment. The main features of the algorithm include a preprocessing step that reduces the size of the input spectrum and an efficient local optimization. In experimental tests, the algorithm performed very well against existing algorithms. The algorithm also performed very well on a large data set generated in this paper from real genomes data.",

author = "Bui, {Thang N.} and Youssef, {Waleed A.}",

year = "2004",

doi = "10.1007/978-3-540-24855-2_104",

language = "English (US)",

isbn = "3540223436",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

publisher = "Springer Verlag",

pages = "908--919",

editor = "Riccardo Poli and Owen Holland and Wolfgang Banzhaf and Hans-Georg Beyer and Edmund Burke and Paul Darwen and Dipankar Dasgupta and Dario Floreano and James Foster and Mark Harman and Lanzi, {Pier Luca} and Lee Spector and Tettamanzi, {Andrea G. B.} and Dirk Thierens and Tyrrell, {Andrew M.}",

booktitle = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

address = "Germany",

}

Bui, TN & Youssef, WA 2004, An enhanced genetic algorithm for DNA sequencing by hybridization with positive and negative errors. in R Poli, O Holland, W Banzhaf, H-G Beyer, E Burke, P Darwen, D Dasgupta, D Floreano, J Foster, M Harman, PL Lanzi, L Spector, AGB Tettamanzi, D Thierens & AM Tyrrell (eds), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 3103, Springer Verlag, pp. 908-919. https://doi.org/10.1007/978-3-540-24855-2_104

An enhanced genetic algorithm for DNA sequencing by hybridization with positive and negative errors. / Bui, Thang N.; Youssef, Waleed A.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ed. / Riccardo Poli; Owen Holland; Wolfgang Banzhaf; Hans-Georg Beyer; Edmund Burke; Paul Darwen; Dipankar Dasgupta; Dario Floreano; James Foster; Mark Harman; Pier Luca Lanzi; Lee Spector; Andrea G. B. Tettamanzi; Dirk Thierens; Andrew M. Tyrrell. Springer Verlag, 2004. p. 908-919 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3103).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

TY - CHAP

T1 - An enhanced genetic algorithm for DNA sequencing by hybridization with positive and negative errors

AU - Bui, Thang N.

AU - Youssef, Waleed A.

PY - 2004

Y1 - 2004

N2 - This paper describes a genetic algorithm for the DNA sequencing problem. The algorithm allows the input spectrum to contain both positive and negative errors as could be expected from a hybridization experiment. The main features of the algorithm include a preprocessing step that reduces the size of the input spectrum and an efficient local optimization. In experimental tests, the algorithm performed very well against existing algorithms. The algorithm also performed very well on a large data set generated in this paper from real genomes data.

AB - This paper describes a genetic algorithm for the DNA sequencing problem. The algorithm allows the input spectrum to contain both positive and negative errors as could be expected from a hybridization experiment. The main features of the algorithm include a preprocessing step that reduces the size of the input spectrum and an efficient local optimization. In experimental tests, the algorithm performed very well against existing algorithms. The algorithm also performed very well on a large data set generated in this paper from real genomes data.

UR - http://www.scopus.com/inward/record.url?scp=33748789402&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33748789402&partnerID=8YFLogxK

U2 - 10.1007/978-3-540-24855-2_104

DO - 10.1007/978-3-540-24855-2_104

M3 - Chapter

AN - SCOPUS:33748789402

SN - 3540223436

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 908

EP - 919

BT - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

A2 - Poli, Riccardo

A2 - Holland, Owen

A2 - Banzhaf, Wolfgang

A2 - Beyer, Hans-Georg

A2 - Burke, Edmund

A2 - Darwen, Paul

A2 - Dasgupta, Dipankar

A2 - Floreano, Dario

A2 - Foster, James

A2 - Harman, Mark

A2 - Lanzi, Pier Luca

A2 - Spector, Lee

A2 - Tettamanzi, Andrea G. B.

A2 - Thierens, Dirk

A2 - Tyrrell, Andrew M.

PB - Springer Verlag

ER -

Bui TN, Youssef WA. An enhanced genetic algorithm for DNA sequencing by hybridization with positive and negative errors. In Poli R, Holland O, Banzhaf W, Beyer HG, Burke E, Darwen P, Dasgupta D, Floreano D, Foster J, Harman M, Lanzi PL, Spector L, Tettamanzi AGB, Thierens D, Tyrrell AM, editors, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Springer Verlag. 2004. p. 908-919. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-540-24855-2_104

An enhanced genetic algorithm for DNA sequencing by hybridization with positive and negative errors

Abstract

Publication series

All Science Journal Classification (ASJC) codes

Access to Document

Other files and links

Fingerprint

Cite this