Optimization in Sanger sequencing
| Autor: | Ángeles Saavedra Places, Silvia Lorenzo-Freire, Ana Cerdeira-Pena, Luisa Carpente |
|---|---|
| Rok vydání: | 2019 |
| Předmět: |
Sanger sequencing
0209 industrial biotechnology 021103 operations research Optimization problem General Computer Science Heuristic (computer science) Heuristic Computer science 0211 other engineering and technologies 02 engineering and technology Management Science and Operations Research chemistry.chemical_compound symbols.namesake 020901 industrial engineering & automation chemistry Modeling and Simulation Simulated annealing symbols Algorithm DNA |
| Zdroj: | Computers & Operations Research. 109:250-262 |
| ISSN: | 0305-0548 |
| DOI: | 10.1016/j.cor.2019.05.011 |
| Popis: | The main objective of this paper is to solve the optimization problem that is associated with the classification of DNA samples in PCR plates for Sanger sequencing. To achieve this goal, we design an integer linear programming model. Given that the real instances involve the classification of thousands of samples and the linear model can only be solved for small instances, the paper includes a heuristic to cope with bigger problems. The heuristic algorithm is based on the simulated annealing technique. This algorithm obtains satisfactory solutions to the problem in a short amount of time. It has been tested with real data and yields improved results compared to some commercial software typically used in (clinical) laboratories. Moreover, the algorithm has already been implemented in the laboratory and is being successfully used. |
| Databáze: | OpenAIRE |
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