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© Oxford University Press

Sequential and parallel algorithms for DNA sequencing

Jacek Blazewicz 1,4, Janusz Kaczmarek 1, Marta Kasprzak 1, Wojciech T. Markiewicz 2 and Jan Weglarz 1,3

1Institute of Computing Science, Poznan University of Technology ul. Piotrowo 3a, 60-965 Poznan
2Institute of Bioorganic Chemistry, Polish Academy of Sciences ul. Noskowskiego 12/14, 61-704 Poznan
3Poznan Supercomputing and Networking Center Poznan, Poland

4To whom correspondence should be addressed

MOTIVATION: Reconstruction of the original DNA sequence in the sequencing by the hybridization approach (SBH) requires computational support due to a large number of possible combinations.One can notice a lack of algorithms admitting false-negative data and giving in addition all possible solutions.

RESULTS: In this paper, a new method of sequencing has been proposed. An algorithm based on its idea (for the general case, when some data are missing, like in the real experiment) has been implemented and tested. Authentic DNA sequences have been used for testing. A parallel version of the algorithm has also been implemented and tested. The quality of the reconstruction is satisfactory for the library of oligonucleotides of length between 8 and 12, and 100, 200 and 300 bp long sequences. A way to a further decrease in the computation time is also suggested.

AVAILABILITY: The program is available on the EMBL file server.

CONTACT: E-mail: blazewic{at}poznlv.put.poznan.pl

Received on July 19, 1996; revised on October 9, 1996; accepted on November 22, 1996

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Home page
 INFORMS Journal on ComputingHome page
J. Blazewicz, F. Glover, and M. Kasprzak
DNA Sequencing--Tabu and Scatter Search Combined
INFORMS Journal on Computing, January 1, 2004; 16(3): 232 - 240.
[Abstract] [PDF]


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