A COMPARISON OF TWO DNA SEQUENCING METHODS
Błażewicz Jacek, Gwóźdź Łukasz, Kasprzak Marta, Przysucha Marcin
Institute of Computing Science, Poznań University of Technology
ul. Piotrowo 3a, 60-965 Poznań, Poland
e-mail: blazewic@poznlv.put.poznan.pl
DOI: 10.12921/cmst.1996.02.01.17-32
OAI: oai:lib.psnc.pl:470
Abstract:
In the paper the problem of DNA sequencing is considered. The sequencing method
by Pevzner [8] is analyzed and its generalization, allowing for finding all acceptable
solutions, is described. It is then compared with another method based on a generation of a solution tree [4]
Key words:
References:
1. Bains, W. 1991. Hybridization Methods for DNA Sequencing. Genomics 11, 294-301.
2. Bains, W., and Smith, G.C. 1988. A Novel Method for Nucleic Acid Sequence Determination. J. Theor. Biol. 135, 303-307.
3. Błażewicz, J. (ed.) 1995. Szeregowe i równoległe algorytmy sekwencjonowania łańcuchów DNA. Report, Poznań Supercomputing and Networking Center 1.
4. Błażewicz, J., Kaczmarek, J., Kasprzak, M., Markiewicz, W.T., and Węglarz, J. 1996. Sequential algorithms for DNA sequencing. Computational Methods in Science and Technology, Poznań Supercomputing and Networking Center 1, 31-42. References 31
5. Błażewicz, J., Kaczmarek, J., Kasprzak, M., Markiewicz, W.T., and Węglarz, J. 1996. A note on l-tuple DNA sequencing in incomplete Spectrum case. Submitted to J. Comput. Biol.
6. Drmanac, R., Labat, I., Brukner, I., and Crkvenjakov, R. 1989. Sequencing of Megabase Plus DNA by Hybridization: Theory of the Method. Genomics 4, 114-128.
7. Khrapko, K.R., Lysov, Y.P., Khorlyn, A.A., Shick, V.V., Florentiev, V.L., and Mirzabekov, A.D. 1989. An oligonucleotide hybridization approach to DNA sequencing. FEBS Letters 256, 118-122.
8. Pevzner, P.A. 1989. l-Tuple DNA Sequencing: Computer Analysis. J. Biomol. Struct. Dyn. 7, 63-73.
9. Southern, E.M., Maskos, U., and Elder, J.K. 1992. Analyzing and Comparing Nucleic Acid Sequences by Hybridization to Arrays of Oligonucleotides: Evaluation Using Experimental Models. Genomics 13, 1008-1017.
In the paper the problem of DNA sequencing is considered. The sequencing method
by Pevzner [8] is analyzed and its generalization, allowing for finding all acceptable
solutions, is described. It is then compared with another method based on a generation of a solution tree [4]
Key words:
References:
1. Bains, W. 1991. Hybridization Methods for DNA Sequencing. Genomics 11, 294-301.
2. Bains, W., and Smith, G.C. 1988. A Novel Method for Nucleic Acid Sequence Determination. J. Theor. Biol. 135, 303-307.
3. Błażewicz, J. (ed.) 1995. Szeregowe i równoległe algorytmy sekwencjonowania łańcuchów DNA. Report, Poznań Supercomputing and Networking Center 1.
4. Błażewicz, J., Kaczmarek, J., Kasprzak, M., Markiewicz, W.T., and Węglarz, J. 1996. Sequential algorithms for DNA sequencing. Computational Methods in Science and Technology, Poznań Supercomputing and Networking Center 1, 31-42. References 31
5. Błażewicz, J., Kaczmarek, J., Kasprzak, M., Markiewicz, W.T., and Węglarz, J. 1996. A note on l-tuple DNA sequencing in incomplete Spectrum case. Submitted to J. Comput. Biol.
6. Drmanac, R., Labat, I., Brukner, I., and Crkvenjakov, R. 1989. Sequencing of Megabase Plus DNA by Hybridization: Theory of the Method. Genomics 4, 114-128.
7. Khrapko, K.R., Lysov, Y.P., Khorlyn, A.A., Shick, V.V., Florentiev, V.L., and Mirzabekov, A.D. 1989. An oligonucleotide hybridization approach to DNA sequencing. FEBS Letters 256, 118-122.
8. Pevzner, P.A. 1989. l-Tuple DNA Sequencing: Computer Analysis. J. Biomol. Struct. Dyn. 7, 63-73.
9. Southern, E.M., Maskos, U., and Elder, J.K. 1992. Analyzing and Comparing Nucleic Acid Sequences by Hybridization to Arrays of Oligonucleotides: Evaluation Using Experimental Models. Genomics 13, 1008-1017.
