Graph algorithms for DNA sequencing – origins, current models and the future
| Autor: | Paweł T. Wojciechowski, Marta Kasprzak, Michal Kierzynka, Aleksandra Swiercz, Jacek Blazewicz, Wojciech Frohmberg, Piotr Zurkowski |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Whole genome sequencing Computational model Information Systems and Management Theoretical computer science General Computer Science Computer science DNA sequencing theory Sequence assembly 0102 computer and information sciences Management Science and Operations Research Bioinformatics 01 natural sciences Industrial and Manufacturing Engineering DNA sequencing Graph 03 medical and health sciences chemistry.chemical_compound 030104 developmental biology chemistry Sequencing by hybridization 010201 computation theory & mathematics Modeling and Simulation Graph algorithms DNA |
| Zdroj: | European Journal of Operational Research. 264:799-812 |
| ISSN: | 0377-2217 |
| Popis: | With the ubiquitous presence of next-generation sequencing in modern biological, genetic, pharmaceutical and medical research, not everyone pays attention to the underlying computational methods. Even fewer researchers know what were the origins of the current models for DNA assembly. We present original graph models used in DNA sequencing by hybridization, discuss their properties and connections between them. We also explain how these graph models evolved to adapt to the characteristics of next-generation sequencing. Moreover, we present a practical comparison of state-of-the-art DNA de novo assembly tools representing these transformed models, i.e. overlap and decomposition-based graphs. Even though the competition is tough, some assemblers perform better and certainly large differences may be observed in hardware resources utilization. Finally, we outline the most important trends in the sequencing field, and try to predict their impact on the computational models in the future. |
| Databáze: | OpenAIRE |
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