Abstract
With the development of next generation sequencing (NGS) technology, genomic research now requires analysis at the entire genome level. Because of easy access to very large amounts of data, it is desirable to look at all the data rather than examine individual bases. At this time, data visualization of the entire genome level can be very useful. However, most visualization tools simply visualize the resulting files derived from external analysis systems. In this study, it was possible to intuitively present the entire sequence to a researcher by converting the data for the entire genome into a 3-dimensional plot. In addition, by compressing the information in 3D space with run length encoding and storing it in a skip list, it is possible to perform fast comparison and search sequences with low complexity by layering base information. As a result, compared to alignment-based sequence comparisons, we obtained improved search results, and we could examine sequences from various angles using layered information.
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Acknowledgment
This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2017R1D1A1A02018504).
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Lee, DY., Tak, HS., Cho, HG. (2019). Sequence Searching and Visualizing over 3D Random Plot of Whole Genome Using Skip List. In: Lee, S., Ismail, R., Choo, H. (eds) Proceedings of the 13th International Conference on Ubiquitous Information Management and Communication (IMCOM) 2019. IMCOM 2019. Advances in Intelligent Systems and Computing, vol 935. Springer, Cham. https://doi.org/10.1007/978-3-030-19063-7_64
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DOI: https://doi.org/10.1007/978-3-030-19063-7_64
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