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Volume 3 (1) 1997, 7-17

PARAMETER ANALYSIS OF CLUSTERS OF MELTING TEMPERATURES OF DNA CHAINS

Błażewicz Jacek 1, Cysewska-Sobusiak Anna 2, Lerczak Agata 1, Kasprzak Marta 1, Markiewicz Wojciech T. 3

1Institute of Computing Science, Poznań University of Technology,
Piotrowo 3a, PL-60965 Poznań, Poland, E-mail: blazewic@sol.put.poznan.pl
2Institute of Electronics and Telecommunications, Poznań University of Technology,
Piotrowo 3a, PL-60965 Poznań, Poland, E-mail: cysewska@et.put poznan.pl
3Institute of Bioorganic Chemistry, Polish Academy of Sciences,
Noskowskiego 12, PL-61704 Poznań, Poland. E-mail: markwt.@ibch.poznan.pl

DOI:   10.12921/cmst.1997.03.01.07-17

OAI:   oai:lib.psnc.pl:478

Abstract:

In the paper the problem of DNA sequencing by hybridization (SBH) is considered.
With the developed software, MELTEM, several assembling procedures are used to ease a collecting a subset of oligonucleotides that would melt under practically identical conditions in a hybridization experiment. Some clustering approaches implemented in the program are compared. The algorithms of MELTEM are presented as well as the selected examples of a melting temperature analysis.

Key words:

clustering, DNA sequencing, hybridization experiment

References:

[1] Rychlik, W., Rhoads, R.E., (1989) Nucleic Acids Res., 17(21), pp. 8543-8551.
[2] Rychlik, W., OLIGO – version 3.4-221, DNA/RNA Primer Selection Software, 1989.
[3] Cantor, C.R., Schimmel, P.R., Biophysical Chemistry. Part III, W.H. Freeman and Co.,
San Francisco 1980.
[4] Breslauer, K.J., Frank, R, Blocker, H., Marky, L.A., (1986) Proc. Natl. Acad. Sci.U.S.A.,
83, pp. 3746-3750.
[5] Anderberg, M.R., Cluster analysis for applications, Academic Press, New York 1973.
[6] Sneath, P.H.A., Sokal, R.R., Numerical taxonomy, W.H. Freeman, San Francisco 1973.
[7] Hartigan, J.A., Clustering algorithms, J. Wiley & Sons, New York 1975.
[8] Kucharczyk, J., Algorytmy analizy skupień w języku ALGOL 60, PWN, Warszawa 1982.

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