• Proceedings of the Korean Information Science Society Conference
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• 2001.04a
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• pp.748-750
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• 2001

최근 Human Genome Project(HGP)에서 사람의 염기 서열의 초안이 발표되었다. 생물체의 염기 서열을 분석하는 방법은 매우 많은데, 그 중 하나가 k-mer 분석이다. k-mer는 유전자의 염기 서열내의 길이가 k인 연속된 염기 서열이다. k-mer 분석은 염기서열이 가진 k-mer들의 빈도의 분포나 대칭성 등을 탐색하는 것이다. 그런데 유전자의 염기 서열은 대용량 텍스트이고 k가 줄 때 기존의 온메모리 알고리즘으로는 처리가 불가능하므로 효율적인 자료구조와 알고리즘이 필요하다. 본 논문에서는 패턴 일치(pattern matching)에 적합하고 외부 메모리를 지원하는 스트링 B-트리(string B-tree)를 이용한 k-mer 분석 방법을 제시하고, 그것을 구현하였으며 몇 가지 실험 결과에 대하여 기술한다.

• The KIPS Transactions:PartA
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• v.8A no.4
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• pp.509-516
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• 2001

As results of many genome projects, genomic sequences of many organisms are revealed. Various methods such as global alignment, local alignment are used to analyze the sequences of the organisms, and k -mer analysis is one of the methods for analyzing the genomic sequences. The k -mer analysis explores the frequencies of all k-mers or the symmetry of them where the k -mer is the sequenced base with the length of k. However, existing on-memory algorithms are not applicable to the k -mer analysis because a whole genomic sequence is usually a large text. Therefore, efficient data structures and algorithms are needed. String B-tree is a good data structure that supports external memory and fits into pattern matching. In this paper, we improve the string B-tree in order to efficiently apply the data structure to k -mer analysis, and the results of k -mer analysis for C. elegans and other 30 genomic sequences are shown. We present a visualization system which enables users to investigate the distribution and symmetry of the frequencies of all k -mers using CGR (Chaotic Game Representation). We also describe the method to find the signature which is the part of the sequence that is similar to the whole genomic sequence.

• The KIPS Transactions:PartA
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• v.9A no.3
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• pp.387-398
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• 2002

As whole genome sequences of many organisms have been revealed by small-scale genome projects, the intensive research on individual genes and their functions has been performed. However on-memory algorithms are inefficient to analysis of whole genome sequences, since the size of individual whole genome is from several million base pairs to hundreds billion base pairs. In order to effectively manipulate the huge sequence data, it is necessary to use the indexed data structure for external memory. In this paper, we introduce a workbench system for analysis and visualization of whole genome sequence using string B-tree that is suitable for analysis of huge data. This system consists of two parts : analysis query part and visualization part. Query system supports various transactions such as sequence search, k-occurrence, and k-mer analysis. Visualization system helps biological scientist to easily understand whole structure and specificity by many kinds of visualization such as whole genome sequence, annotation, CGR (Chaos Game Representation), k-mer, and RWP (Random Walk Plot). One can find the relations among organisms, predict the genes in a genome, and research on the function of junk DNA using our workbench.

• Journal of the Korea institute for structural maintenance and inspection
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• v.21 no.1
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• pp.59-66
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• 2017

In this paper, to protect the piping in nuclear power plants and various plant facilities, we have developed a damper using the friction method and carried out a study to analyze the performance. Friction typed damper means a device for attenuating vibration by generating a frictional force to the bearing and the shaft by applying a compressive force to the MER-Spring. In order to analyze the performance of the damper, the properties of MER-Spring and friction materials were analyzed, a study on the effects of friction was carried out, and the behavior of this equation was established. And, to determine whether deformation of the material and to examine the reliability of the behavior equation established, prototypes was produced and, through a performance test and finite element analysis of a damper made of specimens, they were analyzed. As a result, it is noted that the reliability of the material was confirmed, the coefficient of friction have to be adjusted according to the velocity, cyclic loading test and finite element analysis results show exhibits excellent results. In addition, a review of the dynamic loads in the future shall be performed for the usage in more broad fields.

• Korean Journal of Clinical Laboratory Science
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• v.51 no.4
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• pp.468-474
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• 2019

Deep brain stimulation (DBS) is an effective surgical procedure for treating drug refractory movement disorders, and DBS involves delivering high frequency electrical stimulation to deep brain nuclei. Microelectrode recording (MER) is a complementary test that can precisely identify the location of deep brain nuclei, along with MRI correlation, during DBS surgery to improve the surgical outcome and minimize side effects. The purpose of this paper is to analyze the neuro-physiological waveforms and identify the usefulness of MER by analyzing the MER performed during DBS surgery for treating movement disorders. We retrospectively reviewed 28 patients who underwent MER during DBS surgery for movement disorders from January to December 2018. Of the 28 patients, 38 MERs for the subthalamic nucleus (STN), 10 MERs for the globuspallidusinternus (Gpi), and 4 MERs for the ventral intermediate thalamic nucleus (VIM) were performed. In all the cases, the target sites were found and micro-stimulations were used to check for side effects and to readjust the target sites. The clinical symptoms of all 28 patients improved after surgery. In conclusion, MER is a useful test that employs neuro-physiological waveforms to accurately identify the deep brain nuclei, along with MRI correlation, to improve the DBS surgical outcomes for movement disorders and to minimize side effects.

• Korean Journal of Plant Resources
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• v.19 no.2
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• pp.374-380
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• 2006

With the aim of inducing mutation in fern Cyrtomium caryoptideum var. coreanum, rhizome segments of In vitro-grown cultures were treated with chemical mutagens such as EMS, NMU and colchicine. Based on regeneration ratios, sensitivities for each treatments were assessed and also optimum treatment condition of each mutagens was explored. Optimum concentration for EMS treatment was considered to be 20 to 50mM and for NMU 5 to 10mM. NMU was found to be more effective in inducing chlorophyll and morphological variations than EMS. The RAPD were performed to check the genetic modification of phenotypical variants. As a result, polymorphic DNA band patterns between wild type and variants were observed by two 10-mer primers.

• Journal of Mushroom
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• v.14 no.4
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• pp.174-178
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• 2016

Simple sequence repeats (SSR), also referred to "microsatellites" consist of tandemly repeated short DNA sequence motifs and have been applied in various marker-based studies. SSRs were isolated and characterized from 'Heuktari' and 'Miso', which are major oyster mushroom cultivars in Korea, by genome sequencing and bioinformatic analysis. The genome sizes of 'Heuktari' and 'Miso' were estimated to be 40.8 and 40.3 Mb, respectively, which are larger than those of other P. ostreatus species (PC9 and PC10) and smaller than those of P. eryngii (KNR2312P5). In total, 949 and 968 SSRs were found in the 'Heuktari' and 'Miso' genomes, respectively. Comparative analysis of five mushrooms including P. ostreatus var. florida (PC9 and PC15) and P. eryngii revealed that the number of SSRs in 'Heuktari' and 'Miso' were the highest among them. All mushrooms studied showed similar SSR distribution patterns. Tri-, hexa-, and octanucleotide motifs accounted for the top three fractions of all SSRs.

• Parasites, Hosts and Diseases
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• v.35 no.4
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• pp.295-298
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• 1997

Genonlic DNA from Metagonimn vokogawci and Metagonimw Miyata type was amplified by polymerase chain reaction based on the random amplification of polymorphic DNA (RAPDI technique. Eight random 10-mer oligonucleotide primers (OPA-02, 5-TGCCGAGCTG-3; OPA-09, 5-GGGTAACGCC-3; OPA-17, 5-GTGATCGCAG-3; OPA-11, 5-CAATCGCCGT-3; OPA-13, 5-CAGCACCCAC-3; OPA-17. 5-GACCGCTrGT-3; OPA-19, 5-CAAACGTCGG-3; OPA-20, 5-GTTGCGATCC-3) WITH A G+C CONTENT FO 60-70% (Kit A. Operon Technologies Inc., California, USAI could produce distinguishable banding patterns between the two Metngonimus species. From the results of this study, it was suggested that Metcsonimus Miyata type has a different DNA sequence from M. WOkQgGUIGi. Key words: Metcgonimw vokognwai, MetnBonimw Miyata type, random amplification of polymorphic DNA (RAPD)

• The Korean Journal of Mycology
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• v.39 no.3
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• pp.180-184
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• 2011

This study was carried out to identify the genetic characteristics among isolates of Paecilomyces spp.and Cordyceps spp. by URP-PCR analysis. Twenty URP (universal rice primer) primers of 20 mer which were designed from repetitive sequence of rice, were used for producing PCR DNA fingerprints of the mushrooms. Of them, 5 URP primers, URP2F, URP2R, URP9F, URP4R, and URP17R amplified genomic DNA of the mushrooms with polymorphic PCR patterns. On isolates of Cordyceps militaris, primers URP1F, URP2R, URP6R and URP17R produced PCR polymorphic bands of 4 types. Isolates of Cordypces sp. that are isolated from different area of Korea were identical to isolate of C. militaris, while other species of Cordypces were different to the PCR profiles. However, the URP primers did not identify the polymorphism of PCR profile on isolates of P. japonica.

• Proceedings of the Korean Information Science Society Conference
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• 2012.06b
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• pp.357-359
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• 2012

초 고성능 바이오 서열 분석 장비 기술의 발달로 대량의 바이오 정보가 쏟아져 나오고 있으며, 바이오산업의 발달로 개인별 유전체 정보에 의한 맞춤의학의 시대가 도래되고 있다. 수많은 서열에 대한 분석에는 많은 저장장치 및 주기억장치가 필요하므로 슈퍼컴퓨터 급의 서버와 대량의 데이터를 빠르게 처리할 수 있는 프로그램이 필요하다. 이러한 분석에는 염기서열 일치 검색과 이를 기반으로 하는 Alignment와 Assembly 분석이 있으며, 이를 수행하는 기존의 알고리즘 및 대부분의 프로그램들은 염기서열을 문자열로 취급하고, 해쉬 인덱스 테이블, Brujin 그래프의 사용, 버러우즈 휠러 변환(BWT) 등의 기법을 활용하여 효율적인 분석을 도모하였다. 본 논문에서는 염기서열을 문자열이 아닌 k-mer 묶음의 정수형 하나로 변환하여 검색함으로써 저장 공간의 크기를 약 28% 이상으로 줄이고 형 변환 상태에서의 검색을 수행할 수 있는 알고리즘을 제안한다. Assembly 분석 프로그램인 CalcGen 프로그램을 개발하여 본 알고리즘의 효용성 및 효율성을 실험을 통해 검증하였다. 이 연구의 결과는 향후 대량의 유전체 염기서열의 효율적 분석과 저장 및 처리에 또 하나의 새로운 접근 방법을 제안하는데에 그 의미를 둘 수 있다.