Abstract
Optical Mapping is a method of DNA sequencing that is used to detect large structural variations in genomes. To create these optical maps a restriction enzyme is mixed with DNA. The enzyme binds to DNA and creates labels called restriction sites. These labels are captured by a camera where they appear as bright spots. This work introduces two methods to find these high-intensity points in optical maps. The first method is trying to find the peaks based only on intensity levels and the second is using a signal-to-noise ratio. Both methods have more than three parameters that can affect the results. Differential evolution and particle swarm optimization were used to find the best parameters that would give the highest accuracy. Bionano results were used as ground truth.
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Acknowledgements
This work has been supported by a grant by the Ministry of Health of the Czech Republic (no. NU21-06-00370), and internal grant projects of VSB-Technical University of Ostrava (SGS projects, grant number SP2022/77).
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Doleží, V., Gajdoš, P., Běhálek, M., Vašínek, M. (2022). Restriction Site Detection in Optical Mapping Data. In: Barolli, L., Miwa, H. (eds) Advances in Intelligent Networking and Collaborative Systems. INCoS 2022. Lecture Notes in Networks and Systems, vol 527. Springer, Cham. https://doi.org/10.1007/978-3-031-14627-5_40
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DOI: https://doi.org/10.1007/978-3-031-14627-5_40
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