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:
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.
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:
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.
