Assembling the SARS-CoV genome -- new method based on graph theoretical approach.
Nowadays, scientists may learn a lot about the organisms studied just by analyzing their genetic material. This requires the development of methods of reading genomes with high accuracy. It has become clear that the knowledge of the changes occurring within a viral genome is indispensable for effective fighting of the pathogen. A good example is SARS-CoV, which was a cause of death of many people and frightened the entire world with its fast and hard to prevent propagation. Rapid development of sequencing methods, like shotgun sequencing or sequencing by hybridization (SBH), gives scientists a good tool for reading genomes. However, since sequencing methods can read fragments of up to 1000 bp only, methods for sequence assembling are required in order to read whole genomes. In this paper a new assembling method, based on graph theoretical approach, is presented. The method was tested on SARS-CoV and the results were compared to the outcome of other widely known methods.
Błazewicz
Jacek
J
Institute of Computing Science, Poznań University of Technology, Poznań, Poland.
Figlerowicz
Marek
M
Formanowicz
Piotr
P
Kasprzak
Marta
M
Nowierski
Bartosz
B
Styszyński
Rafał
R
Szajkowski
Lukasz
L
Widera
Pawł
P
Wiktorczyk
Mariusz
M
D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D016679:Genome, Viral; D023281:Genomics / Q000379:methods*; D008969:Molecular Sequence Data; D045473:Severe acute respiratory syndrome-related coronavirus / Q000235:genetics*