Blog Archives

Computational Aspects of DNA Sequencing by Hybridization – a Survey

Kwarciak Kamil, Radom Marcin, Formanowicz Piotr

Sequencing by hybridization (SBH) is a method of reading DNA sequence from its smaller fragments. Such a method has been proposed in late 1980s and until the emergence of the new generation sequencing it has been widely used and improved. Since the initial, classical approach to SBH, many modific ...

Sequential algorithms for DNA sequencing

Błażewicz Jacek, Kaczmarek Janusz, Kasprzak Marta, Węglarz Jan, Markiewicz Wojciech T.

Reconstruction of the original DNA sequence in sequencing by hybridization approach (SBH) due to a large number of possible combinations requires a computational support. In the paper, a new method of sequencing has been proposed. Two algorithms based on its idea have been implemented and tested: ...

A COMPARISON OF TWO DNA SEQUENCING METHODS

Błażewicz Jacek, Gwóźdź Łukasz, Kasprzak Marta, Przysucha Marcin

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]

PARAMETER ANALYSIS OF CLUSTERS OF MELTING TEMPERATURES OF DNA CHAINS

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

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 ...

DNA sequencing by hybridization with additional information available

Formanowicz Piotr

In classical DNA sequencing by hybridization it is assumed that the information obtained in the biochemical stage of the method is a set of the l-tuples composing the target sequence. It means that the information concerning the number of the repeated l-tuples is not available. Such an assumption ...

Preprocessing and Storing High-Throughput Sequencing Data

Świercz Aleksandra, Bosak Bartosz, Chłopkowski Marek, Hoffa Arkadiusz, Kasprzak Marta, Kurowski Krzysztof, Piontek Tomasz, Błażewicz Jacek

DNA sequencing is a process of recognizing DNA sequences of genomes. The process consists in reading short sequences, that are subsequences of a genome, and merging them into longer sequences, preferably the whole genome. In the first phase even billions of short sequences are read at once. To ...