• Journal of Life Science
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• v.8 no.3
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• pp.279-284
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• 1998

The nucleotide sequences of the 5'-untraslated region(5'-UTR) of Hepatitis G virus(HGV) from sera of Korean patients were determines. When compared to the previously reported isolates, the Korean isolates have higher sequence homology with the Japanese isolates indicating the geographic distribution of HGV variants. Interestingly, three discrete regions which are highly conserved among HGV isolates from the same geographical area, thus could be applied to distinguish HGV isolates from the different areas were noticed in the 5'-UTR. Based on the sequences of these group-specific regions, twenty four different HGV isolates could be classified into 5 groups. By using the group-specific regions, inconsistency in HGV typing when based on the different regions of HGV could be solved.

• Proceedings of the Korean Information Science Society Conference
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• 2011.06b
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• pp.466-469
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• 2011

최근에 등장한 Next Generation Sequencing(NGS)은 전통적인 방법에 비해 빠르고 저비용으로 대용량의 시퀀스 데이터를 이용한 차세대 시퀀싱 기술을 말한다. 이렇게 얻은 NGS 데이터를 분석하는 단계 중에서 alignment 단계는 시퀀서에서 얻은 대량의 read를 참조 염기서열에 맵핑하는 단계로 NGS 데이터 분석의 가장 기본이면서 핵심인 단계이다. alignment 도구는 긴 참조 염기서열을 색인화해서 짧은 read를 빠르게 맵핑하는 용도로 사용된다. 현재 많이 사용되고 있는 일반적인 alignment 도구들은 입력데이터에 대한 별도의 전처리 과정이 없으며 나열된 read를 순차적으로 맵핑하는 단순한 구조를 가지고 있다. 본 논문은 NGS 데이터의 특징 중에 특히 read간의 중복성이 존재하고 이를 이용한 read의 효율적 공통부분 서열을 찾는다. 중복이 가능한 read의 공통부분서열과 read의 관계를 그래프 이론의 Hitting Set 문제로 모델링하고 여러 read가 포함하는 공통 부분서열을 사용해서 alignment 단계의 효율을 높일 수 방법을 제안한다.

• The Journal of the Korea Contents Association
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• v.10 no.7
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• pp.81-87
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• 2010

This paper proposes a G-BLAST(BLAST using Grid Computing) system, an integrated software package for BLAST searches operated in heterogeneous distributed environment. G-BLAST employed 'database splicing' method to improve the performance of BLAST searches using exists computing resources. G-BLAST is a basic local alignment search tool of DNA Sequence using grid computing in heterogeneous distributed environment. The G-BLAST improved the existing BLAST search performance in gene sequence analysis. Also G-BLAST implemented the pipeline and data management method for users to easily manage and analyze the BLAST search results. The proposed G-BLAST system has been confirmed the speed and efficiency of BLAST search performance in heterogeneous distributed computing.

• Microbiology and Biotechnology Letters
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• v.32 no.3
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• pp.218-223
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• 2004

Myxobacteria are Gram-negative soil bacteria known to be a rich source of potentially useful secondary metabolites. We have isolated 204 strains of bacteriolytic myxobacteria from soil samples collected in Korea and determined their 16S rRNA sequences. Sequence analysis of the partially determined 16S rRNA sequences has suggested that 132 isolates (65% of total isolates) belong to the genus Myxococcus and 59 isolates (29% of total isolates) belong to the genus Corallococcus. Meanwhile, 4 isolates appear to be Archangium spp. and the other 4 isolates appear to be Stigmatella spp. Genera of the remained 5 isolates have not been identified because their 16S rRNA sequences are distantly related to those of known myxobacteria.

• Korean Journal of Microbiology
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• v.31 no.3
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• pp.189-196
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• 1993

Nucleotide sequences of nodD and nodA from Bradyrhizobium sp. SNUOOI were determined. The open reading frame (ORF) of nodD was 942 bp in length and encoded 314 amino acids. while ORF of nodA, sequence of which is the first one among legume symbionts Bradyrhizobium, was 630 bp and encoded 210 amino acids. The nucleotide sequence of nodD showed 99.4% homology with nodDI of B. japonicum USDAllO. while that of nodA showed 81.5% with B. sp. (Parasponial. At the 5' of nodYAB operon and nodD, consensus nod box sequences composed of 9 bp unit repeated four times and two times respectively were found. Also an A.T-rich sequence was found at 5' of nodD.

• Korean Journal of Microbiology
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• v.39 no.2
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• pp.67-75
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• 2003

One large topic in comparative genomics is to predict functional annotation by classifying protein sequences. Computational approaches for function prediction include protein structure prediction, sequence alignment and domain prediction or binding site prediction. This paper is on another computational approach searching for sets of homologous sequences from sequence similarity graph. Methods based on similarity graph do not need previous knowledges about sequences, but largely depend on the researcher's subjective threshold settings. In this paper, we propose a genome sequence clustering method of iterative testing and graph decomposition, and a simple method to calculate a strict threshold having biochemical meaning. Proposed method was applied to known bacterial genome sequences and the result was shown with the BAG algorithm's. Result clusters are lacking some completeness, but the confidence level is very high and the method does not need user-defined thresholds.

• Journal of KIISE:Computing Practices and Letters
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• v.16 no.3
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• pp.275-280
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• 2010

A local alignment algorithm finds a substring pair of given two strings where two substrings of the pair are similar to each other. A DNA sequence can consist of not only A, C, G, and T but also N and X where N and X are used when the original bases lose their information for various reasons. In this paper, we present an efficient local alignment algorithm for two DNA sequences including N and X using the affine gap penalty metric. Our algorithm is an extended version of the Kim-Park algorithm and can be extended in case of including other characters which have similar properties to N and X.

• The KIPS Transactions:PartD
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• v.13D no.2 s.105
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• pp.207-214
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• 2006

Though the number of completely sequenced genomes quickly grows in recent years, the methods to predict protein functions by homology from the genomes have not been used sufficiently. It has been a successful technique to construct an OPCs(Orthologous Protein Clusters) with the best reciprocal BLAST hits from multiple complete-genomes. But it takes time-consuming-processes to make the OPCs with manual work. We, here, propose an automatic method that clusters OPs(Orthologous Proteins) from multiple complete-genomes, which is, to be extended, based on INPARANOID which is an automatic program to detect OPs between two complete-genomes. We also Prove all possible clustering mathematically.

• Smart Media Journal
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• v.2 no.4
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• pp.34-40
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• 2013

Rapid sequencing of individual genomes with next generation sequencer opens new horizon to biology and personalized medicine. The analyzed sequences help to check several genomic abnormality, genomic expression, epigenomic phenotypes, gene annotation after assembly of their reads. Several trials integrating genomic information and clinical data will assist disease diagnostics and clinical treatments. To have a large step towards individualized medicine, development of smart interface linking specialized sequence data to the public is necessary.

• Korean Journal of Microbiology
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• v.40 no.3
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• pp.211-216
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• 2004

A bacterial strain JE-ll found to produce active extracellular phospholipase D (PLD) was selected from the soil isolates. It was identified as Streptomyces somaliensis on the basis of 16S rDNA sequence analysis, morphological and physiological characteristics. The gene (sspld) encoding S. somaliensis PLD was isolated and characterized. The open reading frame was suggested to encode 538 amino acids with a signal peptide of 33 amino acids. The deduced amino acid sequence of the sspld shared a sequence similarity of 70-88％ with PLDs of other Streptomyces sp. so far reported. The PLD converted phosphatidylcholine to phosphatidylglycerol or phosphatidylserine with the yield of 96 to 99％ (㏖/㏖), but did not act on inositol or ethanolamine as a transphosphatidylation donor.