• Proceedings of the Korean Information Science Society Conference
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• 2005.11b
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• pp.244-246
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• 2005

최근 바이오 데이터 분석에는 데이터 양의 급격한 증가와 이에 따른 문제의 복잡성도 함께 증가하고 있다. 이 결과 다양한 분석 툴들의 유연한 조합과 고성능, 고처리 컴퓨팅이 가능한 분석 시스템이 절실히 요구되고 있다. 본 논문에서는 병렬 컴퓨팅 환경을 이용하고 워크플로우 기반에서 다양한 생물정보 분석 툴들을 자유롭게 조합하여 작업을 수행할 수 있는 바이오워크벤치를 소개한다. 바이오워크벤치 내에는 컴퓨팅 자원 및 작업정보에 대한 모니터링 툴, 각 툴 들과 데이터를 손쉽게 가공할 수 있도록 고안된 인터페이싱 툴 워크플로우 디자인 툴을 포함 하고 있다. 이 기능모듈을 활용함으로써 다양한 생물정보 분석 툴을 이용하는 과정에서 효율적인 분석을 수행을 지원하는 바이오 워크벤치의 기능 및 아키텍쳐을 제시한다.

• Journal of Life Science
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• v.25 no.12
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• pp.1347-1353
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• 2015

The fleshy shrimp, Fenneropenaeus chinensis, is the family of Penaeidae and one of the most economically important marine culture species in Korea. However, its genetic characteristics have never been studied. In this study, a total of 240 wild F. chinensis individuals were collected from four locations as follows: Narodo (NRD, n = 60), Beopseongpo (BSP, n = 60), Chaesukpo (CSP, n = 60), and Cheonsuman (CSM, n = 60). Genetic variability and the relationships among four wild F. chinensis populations were analyzed using 13 newly developed microsatellite loci. Relatively high levels of genetic variability (mean allelic richness = 16.87; mean heterozygosity = 0.845) were found among localities. Among the 52 population loci, 13 showed significant deviation from the Hardy–Weinberg equilibrium. Neighbor-joining, principal coordinate, and molecular variance analyses revealed the presence of three subpopulations (NRD, CSM, BSP and CSP), which was consistent with clustering based on genetic distance. The mean observed heterozygosity values of the NRD, CSM, BSP, and CSP populations were 0.724, 0.821, 0.814, and 0.785 over all loci, respectively. These genetic variability and differentiation results of the four wild populations can be applied for future genetic improvement using selective breeding and to design suitable management guidelines for Korean F. chinensis culture.

• Proceedings of the Korea Society of Poultry Science Conference
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• 2003.11a
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• pp.67-68
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• 2003

한국 재래 닭의 유전적 특성 규명 및 기능 유전체 연구의 기초재료를 확보하고자 대량 EST 염기서열 결정 및 생물정보학 분석을 실시하였다. 대량 EST 염기서열 분석을 위한 첫 번째 단계로 재래 닭의 뇌, 비장, 정소, 배아 생식기를 이용하여 cDNA library를 구축하였다. 각각의 library로부터 총 15,121개의 클론을 선정하여 염기서열을 결정하였다. 생물정보학 분석결과 15,121개의 염기서열은 총 10,353개의 contig로 정리되었다. 이들 염기서열을 기존 데이터베이스를 대상으로 tBlastX(http://www.ncbi.nlm.nih.gov/BLAST) 분석을 실시한 결과, 염기서열 중 56 ％가 기존 데이터베이스에 존재하는 유전자와의 상동성을 보였다. 상동성을 보이는 유전자들은 유전자의 구조 및 기능 분석에 이용될 것이고, 상동성을 보이지 않는 유전자들은 microarray와 같은 대량 유전자 발현분석 시스템을 이용하여 선별한 후 기능분석이 실시될 것이다.

• KIISE Transactions on Computing Practices
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• v.20 no.9
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• pp.513-518
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• 2014

It has become possible for small scale laboratories to interpret large scale genomic DNA, thanks to the reduction of the sequencing cost by the development of next generation sequencing (NGS). De novo assembly is a method which creates a putative original sequence by reconstructing reads without using a reference sequence. There have been various study results on de novo assembly, however, it is still difficult to get the desired results even by using the same assembly procedures and the analysis tools which were suggested in the studies reported. This is mainly because there are no specific guidelines for the assembly procedures or know-hows for the use of such analysis tools. In this study, to resolve these problems, we introduce steps to finding whole genome of an unknown DNA via NGS technology and de novo assembly, while providing the pros and cons of the various analysis tools used in each step. We used 350Mbp of Toxocara canis DNA as an application case for the detailed explanations of each stated step. We also extend our works for prediction of protein-coding genes and their functions from the draft genome sequence by comparing its homology with reference sequences of other nematodes.

• Korean Journal of Agricultural Science
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• v.25 no.1
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• pp.68-78
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• 1998

To investigate the genetic polymorphisms and constitutions of blood proteins and enzymes in the Korean native cattle population of National Livestock Cooperatives Federation(NLCF), the genetic variants of transferrin(Tf), post-transferrin-2(pTf-2), albumin(Alb), post-albumin(pAlb), ceruloplasmin(Cp), amylase-I(Am-I) and herroglobin(Hb) were analyzed using the PAGE(polyacrylamide gel electrophoresis) and ST AGE(starch gel electrophoresis) methods. On the genetic variants of the serum proteins, the transferrin(Tf) locus was assumed to be genetically controlled by codominant alleles, Tf A, $D_1$, $D_2$ and E alleles, and the gene frequencies of these were 0.249, 0.248, 0.260 and 0.243, respectively. The post-transferrin locus was observed to be controlled by pTf-2 F and S alleles, and the gene frequencies of these were 0.662 and 0.338, respectively. The post-albumin(pAlb) loci were identified to be controlled by two alleles, pAlb F and S alleles for pAlb locus, and the gene frequncies of these were 0.440 and 0.560 for pAlb F and S alleles, respectively. On the genetic variants of the serum enzymes, ceruloplasmin(Cp) and amylase-I(Am-I) loci were found to be controlled by two alleles, Cp F and S for Cp locus, and Am-I B and C for Am-I locus, and gene frequencies of these were 0.319 and 0.681 for Cp F and S, and 0.871 and 0.120 for Am-I Band C, respectively. On the genetic variants of the hemoglobin(Hb), the distributions of genotypes were 76.5, 21.2 and 2.3% for Hb AA, AB and BB types, and the gene frequnecies for Hb A and B were 0.871 and 0.129, respectively. On the effects of genetic variants of blood proteins, Tf $D_1D_1$, $D_2D_2$ and $D_2E$ genotypes were significantly higher on body weight at 6 month and average daily gain than that of other Tf genotypes.

• Journal of Mushroom
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• v.5 no.1
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• pp.34-38
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• 2007

The white-colored and the dark gray-colored mutants were frequently happened in cultivated areas of Pleurotus ostreatus (Wonhyeong-neutari). These caused conflicts between farmers and spawn companies. Our studies were conducted to elucidate the mechanism of mutagenesis. The results from the studies would provide valuable informations that could be used to prevent the color-related mutation, and also will be applied in breeding programs of P. ostreatus. Oyster mushroom variety, Wonhyeong-neutari, is somatic hybrid of Pleurotus and has genetic makers for arginine, ornithine, proline, riboflavine. Genetic markers analysis of monospore isolates derived from color mutants show identical tendency with that of Wonhyeong-neutari, these results indicate that color mutants were derived from Wonhyeongneutari. Twenty-one and four homokaryons were selected from the white-colored mutant MGL 2205 and gray-colored ASI 2029. All 34 F1 hybrids derived from the white-colored mutant MGL 2205 produce white-color fruiting bodies, indicating that the white color trait is heritable. In the first generation hybrids between the white-colored MGL 2205 and the gray-colored ASI 2029, all 16 hybrids produced pigmented fruiting bodies. Homokaryons isolated from the hybrid MGL 2205 X ASI 2029 were mated with homokaryon tester strains derived from MGL 2205. By these result, we could assumed that white color trait is a heritable character which is controlled by more than one recessive gene.

• Proceedings of the Korean Information Science Society Conference
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• 2002.10c
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• pp.268-270
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• 2002

오늘날 급속하게 발전하는 유전자 분석기술은 유전자 서열(sequence), 단백질의 기능(function) 및 구조(structure)정보와 같은 생명현상의 연구에 필수적인 정보들을 제공하게 되었다. 특히, 인간 유전체 프로젝트의 완성 이후 염기 및 단백질의 서열데이터를 이용하여 유사한 서열데이터의 검색 및 관련 단백질의 기능, 구조 정보들과 같은 생물정보의 종합적인 검색이 요구되고 있다. 하지만 기존 대부분의 통합서열분석시스템들은 단지 관련 정보를 포함하는 데이터 베이스들에 접근하며 서열유사성을 분석한 후, 그 결과를 단순히 디스플레이 하는 것이 대부분 이였다. 부연하면, 기존 통합 서열분석시스템들은 각 데이터베이스로부터 검색된 결과들 간의 명확한 관계를 설명하지 못하여 종합적인 생물정보를 제공하지 못하고 있다. 따라서 본 논문에서는 염기 및 단백질의 서열데이터로부터 서열유사성 검색 및 관련 단백질의 기능, 구조정보에 해당하는 종합적 인 생물정보를 효과적으로 검색, 서비스 할 수 있는 통합 서열분석시스템의 설계, 구현에 관해 기술한다.

• Korean Journal of Animal Reproduction
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• v.23 no.2
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• pp.159-163
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• 1999

Recent development of the molecular biology techniques has made it possible to characterize and analyze early diagnoses of genetic disorders and economic trait loci. In this study, porcine genomic DNA was extracted from both clotted and dried blood to analyze the porcine estrogen receptor (ER) gene by polymerase chain reaction (PCR). By the methods reported here, genomic DNA extracted from clotted or dried blood was efficient enough to detect ER gene by PCR. Moreover, the PCR-RFLP (restriction fragment length polymorphism) of ER gene was identified by PvuII restriction enzyme. Thus the results obtained from this study show that the clotted and dried blood was useful for identification of the certain genotype in a rapid manner with low cost. Importantly, this study implies that the whole blood can be economically utilized in studies of endocrinology, molecular biology, and genetics by obtaining both serum and DNA simultaneously in an efficient manner.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.289-292
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• 2019

Lachnospiraceae bacterium KGMB03038 (=KCTC 15821) belonging to the class Clostridia in phylum Firmicutes, was isolated from a stool sample of a healthy Korean. Herein, we report the complete genome sequence of strain KGMB03038 analyzed using the PacBio Sequel platform. The genome comprises of 3,334,474 bp with G + C content of 47.8%, which includes 3,099 predicted protein-coding genes, 12 ribosomal RNAs, 54 transfer RNAs, and 4 ncRNAs. Genome analysis revealed that strain KGMB03038 possesses a number of genes involved in hydrolysis of carbohydrates, including mono-, di-, and oligo-saccharides, and biosynthesis of various amino acids.

• Journal of Mushroom
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• v.12 no.3
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• pp.181-186
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• 2014

This research was carried out to analyze the genetic variation of 18 wild strain, 2 breed varieties and 20 mutants of Hypsizygus marmoreus by random amplification of polymorphic DNA(RAPD). Also, 3 strains of Lyophyllum decartes and 1 strain of Lyophyllum shimeji were used. These mushrooms were collected from korea, china, Taiwan and Japan. Spores of H. marmoreus JV-2 strain were irradiated by gamma ray for mutagenesis. 40 kind of primers were used for this reaserch. Number of reaction primer were 31. Electrophorectic patterns of RAPD showed genetic variation. In phylogenetic tree, they were divided into seven group. Discriminative differences were observed between wild strain and mutants in H. marmoreus. These results might suggest that these primers and gamma ray irradiation of spores were useful tools for developing new strain for mushroom.