• 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.

• Korean Journal of Microbiology
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• v.35 no.2
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• pp.121-127
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• 1999

An effective computer program for assembling fragments in DNA sequencing has been developed. The program, called SeqEditor (Sequence Editor), is usable on the pcrsonal computer systems of MS-Widows which is the mosl popular operating system in Korea. It c'm recd several sequence file formats such as GenBak, FASTA, and ASCII. In the SeqEditor program, a dynamic programming algorihm is applied to compute the maximalscoring overlapping alignment between each pjlr of fragments. A novel feature of the program is that SeqEdilor implemnents interaclive operation with a graphical user interface. The performance lests of the prograln 011 fragmen1 data from 16s and 18s rDNA sequencing pi-ojects produced saiisIactory results. This program may be useful to a person who has work of time with large-scale DNA sequencing projects.

• Journal of the Korean Institute of Intelligent Systems
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• v.16 no.2
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• pp.222-227
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• 2006

Recently the research for Traveling Salesman Problem (TSP) using DNA computing with massive parallelism has been. However, there were difficulties in real biological experiments because the conventional method didn't reflect the precise characteristics of DNA when it express graph. Therefore, we need DNA sequence generation algorithm which can reflect DNA features and reduce biological experiment error. In this paper we proposed a DNA sequence generation algorithm that applied DNA coding method of evolution model to DNA computing. The algorithm was applied to TSP, and compared with a simple genetic algorithm. As a result, the algorithm could generate good sequences which minimize error and reduce the biologic experiment error rate.

• KIPS Transactions on Software and Data Engineering
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• v.2 no.2
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• pp.107-112
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• 2013

With the progress of NGS technologies, large genome data have been exploded recently. To analyze such data effectively, the assistance of HPC technique is necessary. In this paper, we organized a genome analysis pipeline to call SNP from NGS data. To organize the pipeline efficiently under HPC environment, we analyzed the CPU utilization pattern of each pipeline steps. We found that sequence alignment is computing centric and suitable for parallelization. We also analyzed the performance of parallel open source alignment tools and found that alignment method utilizing many-core processor can improve the performance of genome analysis pipeline.

• Journal of Plant Biotechnology
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• v.38 no.1
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• pp.15-21
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• 2011

We developed 14 transgenic lines of Chinese cabbage (Brassica rapa) harboring the T-DNA border sequences and CryIAc1 transgene of the binary vector 416 using Agrobacterium tumefaciens-mediated DNA transfer. Six lines had single copy cryIAc1 gene and four of them contained no vector backbone DNA. Of the left border (LB) flanking sequences six nucleotides were deleted in transgenic lines 416-2 and 416-3, eleven nucleotides in line 416-9, and 65 nucleotides including the whole LB sequences in line 416-17, respectively. And we defined 499 bp of genomic DNA (gDNA) of transformed Chinese cabbage, and blast results showed 96% homology with Brassica oleracea sequences. PCR with specific primer for the right border (RB) franking sequence revealed 834 bp of PCR product sequence, and it was consisted of 3' end of cryIAc1, nosterminal region and 52 bp of Chinese cabbage genomic DNA near RB. RB sequences were not found and the 58 nucleotides including 21 bp of nos-terminator 3' end were deleted. Also, there were deletion of 10 bp of the known genomic sequences and insertion of 65 bp undefined genomic sequences of Chinese cabbage in the integration site. These results demonstrate that the integration of T-DNA can be accompanied by unusual deletions and insertions both in transgenic and genomic sequences.

• Journal of Plant Biotechnology
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• v.33 no.3
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• pp.153-160
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• 2006

Brassica rape is an important species used as a vegetable, oil, and fodder worldwide. It is related phylogenically to Arabidopsis thaliana, which has already been fully sequenced as a model plant. The 'Multinational Brassica Genome Project (MBGP)'was launched by the international Brassica community with the aim of sequencing the whole genome of B. rapa in 2003 on account of its value and the fact that it has the smallest genome among the diploid Brassica. The genome study was carried out not only to know the structure of genome but also to understand the function and the evolution of the genes comprehensively. There are two mapping populations, over 1,000 molecular markers and a genetic map, 2 BAC libraries, physical map, a 22 cDHA libraries as suitable genomic materials for examining the genome of B. rapa ssp. pekinensis Chinese cabbage. As the first step for whole genome analysis, 220,000 BAC-end sequences of the KBrH and KBrB BAC library are achieved by cooperation of six countries. The results of BAC-end sequence analysis will provide a clue in understanding the structure of the genome of Brassica rapa by analyzing the gene sequence, annotation and abundant repetitive DHA. The second stage involves sequencing of the genetically mapped seed BACs and identifying the overlapping BACs for complete genome sequencing. Currently, the second stage is comprises of process genetic anchoring using communal populations and maps to identify more than 1,000 seed BACs based on a BAC-to-BAC strategy. For the initial sequencing, 629 seed BACs corresponding to the minimum tiling path onto Arabidopsis genome were selected and fully sequenced. These BACs are now anchoring to the genetic map using the development of SSR markers. This information will be useful for identifying near BAC clones with the seed BAC on a genome map. From the BAC sequences, it is revealed that the Brassica rapa genome has extensive triplication of the DNA segment coupled with variable gene losses and rearrangements within the segments. This article introduces the current status and prospective of Korea Brassica Genome Project and the bioinformatics tools possessed in each national team. In the near future, data of the genome will contribute to improving Brassicas for their economic use as well as in understanding the evolutional process.

• Proceedings of the Korea Contents Association Conference
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• 2016.05a
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• pp.193-194
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• 2016

세포사멸(apoptosis)이란 유전자에 의해 제어되는 세포의 능동적인 죽음을 의미하며 진핵세포만이 가지는 기작으로 세포자살을 일컫는 말이다. 단백질 정보 DB인 UNIPROT으로부터 진핵 생물 종의 세포사멸 단백질(apoptotic protein)을 수집하여 아미노산 서열에 대한 서열비교분석(alignment)을 진행하였다. 그 결과에 따라 다양한 종에 걸쳐 그 서열이 유사하게 유지되는 세포사멸 단백질을 중심단백질로 선정하였다. 비교단백체 분석을 통해서 생물 계통도에서 보여지는 생명종과 이들 단백질과의 연계성을 비교 분석함으로써 단순한 진핵세포에서 점진적으로 확대되는 종까지의 세포사멸 과정을 추론하였다.

• Proceedings of the Korean Information Science Society Conference
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• 2004.04a
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• pp.976-978
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• 2004

Chaining 알고리즘은 주어진 match 정보로부터 좋은 match 조합을 찾아내는 일종의 alignment 알고리즘으로 유전체 서열을 비교하는데 다양하게 응용되고 있다. 특히 서열 전체를 비교하는 대신 부분 서열을 비교할 때 사용할 수 있는 local chaining 알고리즘이 제안되었는데 본 논문은 이 기본적인 알고리즘이 Smith-waterman 알고리즘과 유사하며 따라서 비슷한 단점을 가지고 있음을 지적한다. 그리고 이를 해결하기 위해 X-drop과 정규화 된 정수를 고려하는 두 가지 기법을 적용하고 실험을 통해 개선 효과를 보인다.

• Proceedings of the Korean Information Science Society Conference
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• 2001.04a
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• pp.757-759
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• 2001

생물체가 생명을 영위하기 위해 수행하는 모든 기능들에 대한 정보는 각 개체가 가지고 있는 유전체가 들어있다. 그런데 각 생물체마다, 심지어는 한 생물체의 서로 다른 염색체마다 그 전체 염기서열에서의 base-composition은 같지 않고, 또한 이 구성비에는 일정한 특징이 있다. 따라서 이 논문에서는 각 생물체들의 전체 염기서열을 구성하는 염기의 구성비에 대해 조사하고 비교해 보고자 한다.

• Proceedings of the Korean Information Science Society Conference
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• 2001.04a
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• pp.751-753
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• 2001

지금까지 인간이나 다른 생물체의 전체 유전체 염기서열을 밝혀내는 작업은 크게 세가지 방법으로 진행되었다. Clone-by-clone approach, sequence tagged connector approach, random shotgun approach[1]가 그것인데 마지막의 random shotgun approach는 fragment assembly problem을 비롯한 여러 가지 전산학적인 문제들을 수반한다. 미생물체의 전체 염기서열을 random shotgun approach를 이용하여 밝혀낼 때 몇 가지 전산학적인 문제가 테크닉이 필요하며 그 중에서도 서열간의 forward, reverse의 mating 정보를 이용하는 것이 중요하다. 본 논문은 이러한 mating 작업을 한 눈에 볼 수 있게 하는 소프트웨어 페키지 “Mater”에 대해 소개하고자 하며 그 의미에 대해 논하고자 한다.