J. Blazewicz, J. Kaczmarek, M. Kasprzak, W.T. Markiewicz, J. Weglarz,
"Sequential and parallel algorithms for DNA sequencing", Computer Applications in
the Biosciences 13, 1997, pp. 151-158.
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Abstract:
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. 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.
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8 Sep 1998