• The Transactions of The Korean Institute of Electrical Engineers
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• v.66 no.6
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• pp.955-961
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• 2017

In this paper, we propose a parallel approximate string matching algorithm with k-mismatches for multiple fixed-length patterns (PMASM) in DNA sequences. PMASM is developed from parallel single pattern approximate string matching algorithms to effectively calculate the Hamming distances for multiple patterns with a fixed-length. In the preprocessing phase of PMASM, all target patterns are binary encoded and stored into a look-up memory. With each input character from the input string, the Hamming distances between a substring and all patterns can be updated at the same time based on the binary encoding information in the look-up memory. Moreover, PMASM adopts graphics processing units (GPUs) to process the data computations in parallel. This paper presents three kinds of PMASM implementation methods in GPUs: thread PMASM, block-thread PMASM, and shared-mem PMASM methods. The shared-mem PMASM method gives an example to effectively make use of the GPU parallel capacity. Moreover, it also exploits special features of the CUDA (Compute Unified Device Architecture) memory structure to optimize the performance. In the experiments with DNA sequences, the proposed PMASM on GPU is 385, 77, and 64 times faster than the traditional naive algorithm, the shift-add algorithm and the single thread PMASM implementation on CPU. With the same NVIDIA GPU model, the performance of the proposed approach is enhanced up to 44% and 21%, compared with the naive, and the shift-add algorithms.

• Archives of design research
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• v.19 no.2 s.64
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• pp.241-250
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• 2006

Hangeul as the Korean unique characters were invented according to some character-making principles and based on scholars' exhaustive researches. While most of the characters in the world evolved naturally, Hangeul was invented based on a precise linguistic analysis of the time, and therefore, it is most scientific and reasonable among various characters throughout the world. Nevertheless, Hangeul typeface designs do not seem to inherit the ideology of scientific and reasonable Hangeul correctly. For the square forms have been used intact due to the influences from the Chinese characters which prevailed during the time. If a single set of square characters should be designed, as much as 11,172 fonts should be designed, which suggests that advantages of Mangeul may not well be used fully; Hangeul was invented to visualize every sound with the combinations of 28 vowels and consonants. Problems of such square fonts began to be identified since 1900's when typewriters were introduced first from the West. Since a typewriter is designed with 28 characters laid out on its keyboard by using such combinations, the letters may be easily combined on it. The so-called the flexibility square-format typeface was born as such. Specially, the three-pairs fonts of these can be combined up to 67 letters including vowels and consonants. The three-pairs fonts system can help to solve the problems arising form the conventional square fonts and inherit the original ideology of Hangeul invention. This study aims to review the history of the three-pairs fonts designs facilitated by mechanic encoding of Hangeul and thereupon, suggest some desirable directions for future Hangeul fonts. Since the flexibility square-format typeface is expected to evolve more and more owing to development of the digital technology, they would serve our age of information in terms of both functions and convenience. Just as Hunminjongum tried to be literally independent from the Chinese characters, so the flexibility square-format typeface designs would serve to recover identity of our Hangeul font designs.