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Experimental Analysis of Recent Works on the Overlap Phase of De Novo Sequence Assembly
Jihyuk Lim, Sun Kim, Kunsoo Park
http://doi.org/10.5626/JOK.2018.45.3.200
Given a set of DNA read sequences, de novo sequence assembly reconstructs a target sequence without a reference sequence. For reconstruction, the assembly needs the overlap phase, which computes all overlaps between every pair of reads. Since the overlap phase is the most time-consuming part of the whole assembly, the performance of the assembly depends on that of the overlap phase. There have been extensive studies on the overlap phase in various fields. Among them, three state-of-the-art results for the overlap phase are Readjoiner, SOF, and Lim-Park algorithm. Recently, a rapid development of sequencing technology has made it possible to produce a large read dataset at a low cost, and many platforms for generating a DNA read dataset have been developed. Since the platforms produce datasets with different statistical characteristics, a performance evaluation for the overlap phase should consider datasets with these characteristics. In this paper, we compare and analyze the performances of the three algorithms with various large datasets.
A Malicious Traffic Detection Method Using X-means Clustering
Myoungji Han, Jihyuk Lim, Junyong Choi, Hyunjoon Kim, Jungjoo Seo, Cheol Yu, Sung-Ryul Kim, Kunsoo Park
Malicious traffic, such as DDoS attack and botnet communications, refers to traffic that is generated for the purpose of disturbing internet networks or harming certain networks, servers, or hosts. As malicious traffic has been constantly evolving in terms of both quality and quantity, there have been many researches fighting against it. In this paper, we propose an effective malicious traffic detection method that exploits the X-means clustering algorithm. We also suggest how to analyze statistical characteristics of malicious traffic and to define metrics that are used when clustering. Finally, we verify effectiveness of our method by experiments with two released traffic data.
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