• Proceedings of the Korea Information Processing Society Conference
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• 2004.11a
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• pp.697-700
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• 2004

서열의 유사성 검색에 잘 알려진 도구로는 BLAST 와 FASTA 가 있으며 이들 알고리즘은 알려지지 않은 유기체를 sequencing 작업을 통하여 얻어진 염기서열과 유전자 데이터베이스를 대상으로 유사성을 검색한다. 이때 서열의 유사성을 검색하기에 앞서 선행 되어야만 하는 sequencing작업은 시간적인 면에서 상당한 비용을 요구한다. 반면 sequencing 작업을 하기 않고도 간단한 실험에 의해 얻을 수 있는 부분적인 서열정보만을 대상으로 데이터베이스에서 검색 할 수 있는 알고리즘으로 RIFLE가 있다. 본 논문에서는 RIFLE 알고리즘을 구현하고 실험데이터를 생성하여 성능에 대한 분석 평가를 하고자 한다. 성능평가 결과 RIFLE 알고리즘은 시간복잡도 $O(n^2)$으로 빠른 반면 일부 서열에 있어서 실제 유사도에 비해 정확도가 낮게 평가되는 결과가 산출되었다.

• Proceedings of the Korean Information Science Society Conference
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• 2004.04b
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• pp.295-297
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• 2004

유전자의 생물학적 기능을 밝히고 세포 내 상호작용을 이해하는 것은 post-genome era의 가장 중요한 작업 중 하나이다. 이러한 세포 내 상호작용은 복잡한 생화학적 네트워크를 형성하게 되며 그 중 Metabolic pathway(대사 경로)는 생물 시스템을 이해하는데 가장 중요한 부분을 차지하게 된다. 대사 경로를 분석하기 위하여 분자의 기능 및 생화학적 프로세스에 대한 정보를 데이터베이스에 저장.관리해야하고, 사용자의 다양한 질의에 대하여 관련정보를 검색하여 GUI환경에서 제공해야 한다. 이 논문은 대사 경로 정보를 객체 데이타베이스 형태로 모델링하여 구축하고, 사용자가 관심있는 정보를 SBML형태로 제공하는 대사경로 데이타베이스의 설계 및 구현에 관해 다룬다.

• Journal of Intelligence and Information Systems
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• v.14 no.2
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• pp.193-206
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• 2008

Medical diagnosis can be considered a classification task which classifies disease types from patient's condition data represented by a set of pre-defined attributes. This study proposes a hybrid genetic algorithm based classification method to develop classifiers for multidimensional pattern classification problems related with medical decision making. The classification problem can be solved by identifying separation boundaries which distinguish the various classes in the data pattern. The proposed method fits a finite number of regional agents to the data pattern by combining genetic algorithms and local adaptive operations. The local adaptive operations of an agent include expansion, avoidance and relocation, one of which is performed according to the agent's fitness value. The classifier system has been tested with well-known medical data sets from the UCI machine learning database, showing superior performance to other methods such as the nearest neighbor, decision tree, and neural networks.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.16 no.10
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• pp.6715-6721
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• 2015

Recently, DNA data of missing person, killed person, and missing child continue to increase but most of statistical calculation for paternity confirmation is being done through manual methods or Excel. Therefore, we need development of a software which is able to facilitate both systematic management and effective analysis of Short Tandem Repeat (STR) derived from DNA data. Without extensive testing, through a twenty-month study was developed a web-based system which performs paternity analysis and kinship analysis easily based on the various options. The former uses an existing algorithm for paternity index and the latter does Identity by descent (IBD) formula. Due to our system validated over real datasets in terms of likelihood ratio and probability of paternity, it ensures increased reliability as well as effective management and analysis of DNA data in mass disaster. In addition, it includes advanced features such as an integrated environment, user-centered interface, process automation and so on.

• Journal of Life Science
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• v.12 no.2
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• pp.219-225
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• 2002

The organization of eukayotic chromatin into specific conformation that are associated with transcription, replication, reapir and other nuclear processes are achieved via a series of DNA-protein interaction. These interactions are mediated by a range of DNA-binding domains such as SAP domain et at. By searching S. pombe genomic DNA database, we have found a gene named SAPuvs (SAP UV Sensitive) whose amino acid sequence is in part similar to SAP domain of Arabidopsis poly (ADP-ribose) polymerase and Ku7O. Knock-out cell of S. pombe SAPuvs gene was constructed using Ura4 as a selection marker. Survival analysis of knock-out cell indicated that treatment with UV significantly reduces the survival compared to wild type cell. Potentiation of MMS-induced cytotoxicity by 3AB post-treatment was observed in wild type cells, but not in knock-out cells. These data suggested that the protein encoded by SAPuvs gene is associated with chromatin reorganization during DNA repair.

• The Korean Journal of Mycology
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• v.43 no.1
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• pp.33-39
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• 2015

In filamentous fungi, velvet complex associated with the veA gene plays pivotal roles in development and secondary metabolism. In a model fungus Aspergillus nidulans, many proteins that can interact with VeA, including two methyltransferases VipB and VipC, have been isolated and characterized. In this study, we isolated homologs of the vipB and vipC genes in the human opportunistic pathogenic fungus Aspergillus fumigatus and named AfuvipB and AfuvipC. The AfuvipB gene, annotated as Afu3g14920 in the Aspergillus Genome Database (AspGD) database, consists of 1,510 bp interrupted with 10 introns yielding 336 amino acid-long putative methyltransferase protein. Similarly, AfuvipC, which is Afu8g01930, has 10 introns and encodes a polypeptide with 339 amino acids having a methyltransferase domain in the middle of the protein. To characterize the function of the genes in A. fumigatus, knock-out mutants were generated and the phenotypes were observed. Deletion of AfuvipB gene caused no obvious phenotypic change on point inoculation but showed smaller colony than wild-type when the mutant was subjected to culture on single spore-driven culture condition. However, AfuvipC deletion mutant demonstrated no phenotypic difference from wild type both in point inoculation and streaking cultures. These results indicate that the two methyltransfereases might have a redundant role and could be dispensable in normal culture conditions.

• Proceedings of the Korean Information Science Society Conference
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• 2007.06a
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• pp.25-26
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• 2007

• Proceedings of the Korean Information Science Society Conference
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• 2004.04b
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• pp.292-294
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• 2004

최근 pathway 정보의 중요성에 점점 커지고 있다. 하지만 이런 정보를 이용하기에 많은 문제점이 발생하고 있다. 이런 문제점의 해결 방법으로 웹 서비스가 도입되고 있다. 이 논문에서는 주요 pathway 데이터베이스 중 하나인 BIND와 체계적인 개념으로 유전자 용어를 정리한 Gene Ontology(GO)에 대한 웹 서비스를 개발하였다. 개발자들은 이 웹 서비스를 이용하여 BIND와 GO 데이터를 보다 쉽게 이용할 수 있을 것이다.

• Proceedings of the Korea Information Processing Society Conference
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• 2008.11a
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• pp.364-366
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• 2008

본 논문에서는 지놈 연구에서 반드시 필요한 유전체 서열정보의 상동성 검색을 위해 해외 데이터베이스에만 의존하고 있는 국내 지놈 연구자들에게 더욱 빠르고 쉽게 접근할 수 있는 서열블라스트를 만들 수 있는 방법을 제공함으로써 국내 지놈연구에 도움이되고자 특정 종류의 유전자정보 만을 모아놓은 지놈 서열블라스트 시스템을 설계하고 구현하는 방법을 제시하였다. 이 시스템을 활용하면 많은 생물 지놈 연구자들의 연구시간을 획기적으로 단축할 수 있을 것이다.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.5 no.2
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• pp.157-168
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• 2000

Sea urchin S. intermedius occurring in the Korean east coast is a cold water species that belongs to the family Strongylocentrotidae of Echinoidea. Although it is known that there are nine species in the family, species identification criteria, phylogenetic relationships, time and process of evolution of the family members have not been uncovered clearly. In the present study, I tried to find some clues to such problems for S. intermedius by means of DNA sequences. For this, cytochrome c oxidase subunit I (COI), one of the mitochondrial genes that evolve fast and follow maternal inheritance was analyzed. DNA was extracted from the female gonad of S. intermedius, a segment of COI gene amplified by polymerase chain reaction (PCR), and finally a total of 1077 base pair sequence of COI obtained by cloning and sequencing the PCR product. The sequence was compared with homologous genes of other sea urchins and echinoderm species. Phylogenetic trees of the COI gene segment revealed that S. intenedius is a sister species of S. purpuratus which lives along the east coast of the Paciflc. With reference to the fossil records of sea urchins and genetic distances in the molecular phylogenies, it is estimated that the two species were separated about 0.89 million years ago when the earth temperature fluctuated significantly. The current disjunct distribution patterns of the two species and the climate change of the earth at the time of separation suggest that speciation might have occurred by vicariance. The COI gene sequence obtained here now can be used as a molecular character which discerns S. intermedius from the other sea urchin species of Strongylocentrotidae.