• Journal of KIISE:Computer Systems and Theory
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• v.32 no.11_12
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• pp.578-586
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• 2005

In this Paper we consider the problem of sequence alignment with quality scores. DNA sequences produced by a base-calling program (as part of sequencing) have quality scores which represent the confidence level for individual bases. However, previous sequence alignment algorithms do not consider such quality scores. To solve sequence alignment with quality scores, we propose a measure of an alignment of two sequences with orality scores. We show that an optimal alignment in this measure can be found by dynamic programming.

• Journal of Korean Ophthalmic Optics Society
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• v.14 no.4
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• pp.89-96
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• 2009

Purpose: This study was to investigate and analyze understanding and knowledge of the eye in biological science education for middle and high school students in Busan. Methods: A total of 821 middle and high school students from four different schools participated by self-administered questionnaire test. The results were compared and analyzed by grade and gender. Results: In the survey of the understanding about the eye in the biological science curriculum, the results indicated that the more learning of the eye in biological science lecture led to the more understanding of the role of the eye. The difference of understanding the eye between learned and unlearned students in biological sciences lecture was significant (p<0.01). In the survey of the knowledge of the eye, students did not know about myopia and astigmatism (average value <50). Conclusions: As biological science education is one of the major factors to understand the role of the eye, this result suggests that more information about the eye in the curriculum of biology is included.

• Proceedings of the Korean Information Science Society Conference
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• 2011.06c
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• pp.228-231
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• 2011

최근 표절에 대한 사회적 관심이 꾸준히 높아지고 있는 가운데, 기계적으로 유사한 문서를 탐색하는 방법에 대한 많은 연구가 이루어지고 있다. 이 중 생물정보학에서 유전자 서열을 분석하기 위해 사용되는 '지역 정렬(local alignment)' 기법은 문서 간 유사 영역을 탐색하는 데에 유용하다. 한편 한글에는 조사가 존재하는데, 이 때문에 한글 문장은 각 품사의 순서에 큰 영향을 받지 않는다. 이러한 한글의 특성을 이용해 기존 문서의 어순만 바꾼 문장을 생성할 경우, 지역 정렬을 이용한 탐색 방법으로는 이를 찾아내기 힘들다. 본 논문에서는 한글의 특성을 고려하여 어순과 관계없이 해당 영역의 유사성을 찾아내는 새로운 한글 유사 문서 탐색 방법을 제시한다. 이를 위하여, 성분 정렬(composition alignment) 기법을 적용한다. 성분 정렬 기법은 생물학에서 생물의 진화 과정이나 돌연변이 DNA 등 서열의 순서가 일부 뒤바뀌는 것을 허용하면서 유사한 시퀀스를 찾는 기법으로 기존의 방법보다 더욱 유연하고 민감한 방법이라 할 수 있다. 이를 적용하여 한글 문서를 탐색한 결과, 일반적인 문장 및 거의 동일한 문장 간의 유사도 점수는 큰 변화가 없었으나, 어순을 바꾼 문장의 경우 기존의 방법보다 평균 35.34% 가량 민감하게 탐색할 수 있었다. 추후 한글에 대한 초성 추출 및 성분 정렬 방법을 응용하여 다단계 구조의 유사 문서 탐색 방법에 대해 연구할 계획이다.

• Journal of KIISE:Computer Systems and Theory
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• v.33 no.5
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• pp.267-281
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• 2006

PPI(Protein-Protein Interaction) data has information about the organism has maintained a life with some kind of mechanism. So, it is used in study about cure research back, cause of disease, and new medicine development. This PPI data has been increased by geometric progression because high throughput methods are developed such as Yeast-two-hybrid, Mass spectrometry, and Correlated mRNA expression. So, it is impossible that a person directly manage and analyze PPI data. Fortunately, PPI data is able to abstract the graph which has proteins as nodes, interactions as edges. Consequently, Graph theory plentifully researched from the computer science until now is able to be applied to PPI data successfully. In this paper, we introduce Proteinca(PROTEin INteraction CAbaret) workbench system for easily managing, analyzing and visualizing PPI data. Proteinca assists the user understand PPI data intuitively as visualizing a PPI data in graph and provide various analytical function on graph theory. And Protenica provides a simplified visualization with gravity-rule.

• The Journal of the Korea Contents Association
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• v.16 no.6
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• pp.260-269
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• 2016

With the development of genomics, wearable device and IT/NT, a vast amount of bio-medical data are generated recently. Also, healthcare industries based on big-data are booming and big-data technology based on bio-medical data is rising rapidly as a core technology for improving the national health and aged society. Also, oriental medicine research is focused with modern research technology and validate it's various biochemical effect by combining with molecular biology technology. However there are few searching system for finding biochemical mechanism which is related to major compounds in oriental medicine. Therefore, in this paper, we collected papers related with medical herbs from PubMed and constructed a medical herbs database to store and manage chemical, gene/protein and biological interaction information extracted by a literature analysis on the papers. Also, to supporting a multidimensional analysis on the database, we developed a network analysis system based on a hierarchy structure of chemical, gene/protein and biological interaction information. Finally, we expect this system will be used the major tool to discover various biochemical effect by combining with molecular biology technology.

• 대한공업교육학회지
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• v.34 no.1
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• pp.252-273
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• 2009

Due to the importance of biotechnological literacy, the educational community in fields such as technology education, science education, and agricultural education has acknowledged the importance of biotechnology instruction for secondary school. Although recognized as a content organizer in the field of technology education, the actual teaching of biotechnology has not been broadly implemented in technology education classes. In the perspective of expectancy-value theory, technology teachers' motivation is the key factor for affecting the biotechnology instruction. This study investigates Korean technology teachers' motivational beliefs toward biotechnology and its instruction and their perceived ability and value toward biotechnology learning contents. To measure their motivational beliefs and attitudes, a composite on-line survey (fifteen motivational beliefs items, eight biotechnology content items, and related demographic items) was developed. Based on 114 Korean technology teachers' responses the researcher performed a descriptive analysis, independent t-test, and factor analyses (exploratory and confirmatory factor analysis using M-plus 5.0 and SPSS 16.0). Korean technology teachers' abilities toward eight biotechnology contents indicated lowscores while their values were relatively high. Through the independent sample t-test by two demographic variables (gender and professional development), this study found several significant differences in the perceived value. As a preliminary finding of exploratory factor analysis, fifteen items was separated into two motivational constructs of expectancy (6 items) and value (8 items). One item (item #6) was eliminated due to the cross loading. The final findings of this study may have significant implications for professional development regarding biotechnology and its instruction (both in-service and pre-service training) of technology teachers. Also, the confirmatory facctor analysis supported the preliminary finding. Finally, this study recommends that a validity test for other population, investigation for motivational sub-constructs, and in-depth investigation toward biotechnology instruction.

• Korean Journal of Ecology and Environment
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• v.51 no.1
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• pp.124-134
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• 2018

We analyzed research topics, temporal distribution of field sites, and researcher network of 1,508 limnology publications in the Korean Journal of Limnology (1968~2012) and the Korean Journal of Ecology and Environment (2013~2017). We found that water quality and sediment, phytoplankton, invertebrates, and fish were major subjects during the study periods. Survey of flora and fauna and physiological experiment of freshwater species were the largest subjects during 1970~80s, while other subjects including production, behavior, modeling, and ecological assessment have been rapidly increased since the 1990s. Most of the biological taxa equally studied lotic and lentic system, however, invertebrates and fish related studies more focused on the lotic system. Spatially, the field site of Korean limnology studies was found to be concentrated in main river channels runs through urban areas and artificial lakes than preserved natural areas. Freshwater system, located at the elevation range of 301~400 m (upstream of main channels), had the lowest number of field sites. Collaboration among researchers and different institution types have been steadily increased and expanded as the number of publications increased.

• Journal of Marine Life Science
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• v.5 no.1
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• pp.17-24
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• 2020

We have identified a heat shock protein 70 gene from freshwater snail, Semisulcospira coreana. The freshwater snail HSP70 gene encode a polypeptide of 639 amino acids. Based on bioinformatic sequence characterization, HSP70 gene possessed three classical signature motifs and other conserved residues essential for their functionality. The phylogenetic analysis showed that S. coreana HSP70 had closet relationship with that of golden apple snails, Pomacea canaliculata. The HSP70 mRNA level was significantly up-regulated in response to thermal and salinity challenges. These results are in agreement with the results of other species, indicating that S. coreana HSP70 used be a potential molecular marker in response to external stressors and the regulatory process related to the HSP70 transcriptional response can be highly conserved among species.

• Proceedings of the Korea Information Processing Society Conference
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• 2006.11a
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• pp.69-72
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• 2006

최근 생명 정보학 기술의 발달로 마이크로 단위의 실험조작이 가능해짐에 따라 하나의 chip상에서 전체 genome의 expression pattern을 관찰할 수 있게 되었고, 동시에 수 만개의 유전자들 간의 상호작용도 연구가능하게 되었다. 이처럼 DNA 마이크로어레이 기술은 복잡한 생물체를 이해하는 새로운 방향을 제시해주게 되었다. 따라서 이러한 기술을 통해 얻어진 대량의 유전자 정보들을 효과적으로 분석하는 방법이 시급하다. 본 논문에서는 마이크로어레이 실험에서 다양한 원인에 의해 발생하는 잡음(noise)을 줄이거나 제거하는 과정인 정규화과정을 거쳐 특징 추출방법인 SVM(Support Vector Machine) 방법을 이용하여 데이터를 2개의 클래스로 나누고, 표준화 방법들의 성능 비교를 위해 Adaptive Simulated Annealing 알고리즘으로 정확도를 평가하는 분류 시스템을 설계 구현하였다.

• Proceedings of the Korea Information Processing Society Conference
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• 2008.11a
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• pp.356-359
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• 2008

최근 생물정보학 분야에서 인간 유전체에 존재하는 CNV(copy number variation)에 관한 연구가 주목 받고 있다. CNV 영역은 1kbp-3Mbp 사리의 서열이 반복되거나 결실되는 변이 영역으로 정의된다. 우리는 선행연구에서 기가 시퀀싱(giga sequencing)의 결과 산출되는 DNA 서열조각인 리드(read)를 레퍼런스 시퀀스에 서열 정렬하여 CNV 영역을 찾아내는 새로운 CNV 검색 방식을 제안하였다. 후속 연구로서 본 논문에서는 DNA 서열에 존재하는 repeat 영역 문제를 해결하기 위한 새로운 방안을 제안하고, 리드의 출현 빈도 정보를 분석하여 CNV 영역을 찾아내는 CNV 영역 검색 알고리즘을 보인다. 제안된 알고리즘 Gaussian 분포를 갖는 출현 빈도 정보로부터 통계적 유의성을 갖는 영역을 추출하여 CNV 영역후보로 하고, 다음 경제 과정을 거쳐 최종의 CNV 영역을 추출한다. 성능 평가를 위하여 프로토타임 시스템을 개발하였으며, 시뮬레이션 실험을 수행하였다. 실험 결과에 의하여 제안된 방식은 반복되거나 결실되는 형태의 CNV 영역을 효율적으로 검출하며, 또한 다양한 크기의 CNV 영역을 효율적으로 검출할 수 있음을 입증한다.