• Korean Journal of Soil Science and Fertilizer
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• v.45 no.6
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• pp.1100-1107
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• 2012

Bacterial endophytes may be important factors in plant growth and ecologically relevant functions in rice. Using pyrosequencing technology, we analyzed the composition of endophytic bacterial communities that colonized the roots of rice cultivated in long-term fertilized (APK) and non-fertilized (NF) paddy soils. A total of 1,900 reads were obtained from 2 samples. All sequences were classified into 177 OTUs (APK sample) or 72 OTUs (NF sample) at a 97% similarity cut-off. Twenty-two OTUs were shared between the 2 samples, and these were also the most dominant OTUs in both samples. Proteobacteria was the most dominant phylum with 90.2%, followed by Actinobacteria (7.1%) and Bacteroidetes (1.1%). Furthermore, Pseudomonas was the most abundant genus in both samples. We observed clear differences in the structure of the endophytic bacterial community structure between the 2 samples. Notably, the distributions of Alphaproteobacteria and Gammaproteobacteria were markedly different. The diversity index of the APK sample was higher than that of the NF sample. These findings showed that the endophytic bacterial community of rice roots was affected by the presence of fertilizers in the rice field soil.

• 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.

• The KIPS Transactions:PartD
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• v.16D no.5
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• pp.661-672
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• 2009

Recently it was found that various genetic structural variations such as CNV(copy number variation) exist in the human genome, and these variations are closely related with disease susceptibility, reaction to treatment, and genetic characteristics. In this paper we propose a new CNV detection algorithm using millions of short DNA sequences generated by giga-sequencing technology. Our method maps the DNA sequences onto the reference sequence, and obtains the occurrence frequency of each read in the reference sequence. And then it detects the statistically significant regions which are longer than 1Kbp as the candidate CNV regions by analyzing the distribution of the occurrence frequency. To select a proper read alignment method, several methods are employed in our algorithm, and the performances are compared. To verify the superiority of our approach, we performed extensive experiments. The result of simulation experiments (using a reference sequence, build 35 of NCBI) revealed that our approach successfully finds all the CNV regions that have various shapes and arbitrary length (small, intermediate, or large size).

• Journal of Internet Computing and Services
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• v.20 no.4
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• pp.21-27
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• 2019

Selection of feature pattern gathered from the observation of the RNA sequencing data (RNA-seq) are not all equally informative for identification of differential expressions: some of them may be noisy, correlated or irrelevant because of redundancy in Big-Data sets. Variable selection of feature pattern aims at differential expressed gene set that is significantly relevant for a special task. This issues are complex and important in many domains, for example. In terms of a computational research field of machine learning, selection of feature pattern has been studied such as Random Forest, K-Nearest and Support Vector Machine (SVM). One of most the well-known machine learning algorithms is SVM, which is classical as well as original. The one of a member of SVM-criterion is Support Vector Machine-Recursive Feature Elimination (SVM-RFE), which have been utilized in our research work. We propose a novel algorithm of the SVM-RFE with Q-learning in reinforcement learning for better variable selection of feature pattern. By comparing our proposed algorithm with the well-known SVM-RFE combining Welch' T in published data, our result can show that the criterion from weight vector of SVM-RFE enhanced by Q-learning has been improved by an off-policy by a more exploratory scheme of Q-learning.

• Electronics and Telecommunications Trends
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• v.32 no.1
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• pp.116-122
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• 2017

유전체 분석을 위한 시퀀싱 기술의 발전으로 유전체 데이터량이 폭발적으로 증가하고 있다. 저장 및 관리 비용 절감을 위해 유전체 데이터 압축 기술이 연구되고 있지만, 국제 표준의 부재로 다양한 포맷들이 사용되고 있다. 최근, MPEG에서 유전체 데이터의 압축 및 저장 표준에 대한 필요성을 받아들여 표준화 작업이 진행 중이다. 본고에서는 유전체 분석의 기본이 되는 염기서열의 분석 과정을 소개하고, 유전체 데이터 압축 및 저장 기술의 표준화 동향에 대해서 살펴보고자 한다.

• Bulletin of Food Technology
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• v.26 no.4
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• pp.344-348
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• 2013

시크제네시스(SeqGenesis)는 2011년 7월 설립된 대전소재 생물정보분석 전문기업으로, 국가 연구기관에서 다수 미생물, 인간, 동물, 식물에 대한 오믹스 통합 데이터베이스 및 생물정보 분석 플랫폼 개발, 영양유전체 연구지원 시스템 구축, 분석알고리즘 개발 등 다양한 생물정보분석에 대한 경력을 가진 전문연구원으로 구성되어 있다. 현재 차세대시퀀싱(NGS)데이터 분석, 마이크로바이옴(microbiome) 분석, 고밀도 마이크로어레이 프로브 디자인 및 분석, 생물 정보 컨설팅, 오믹스 데이터베이스 구축 등 연구 지원 파트너로서 생물정보분석 서비스를 하고 있다.

• Proceedings of the Korea Contents Association Conference
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• 2018.05a
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• pp.323-324
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• 2018

전장 cDNA 클론을 시퀀싱하는 것은 선택적 스플라이싱 형태를 비롯한 정확한 유전자 구조를 정의하는데 유용하게 사용될 수 있으며, 유전자 및 단백질의 생물학적 기능연구에 중요한 자원을 제공한다. 포괄적이며 비 중복적인 cDNA의 생산은 인간 유전체 연구의 중요한 목표이다. 본 연구에서 제공하는 인간 cDNA 라이브러리 분석 파이프라인은 전장 cDNA를 분석하는 자동화 도구로 여러 연구자들에게 활용 될 수 있을 것으로 사료된다.

• Proceedings of the Korea Contents Association Conference
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• 2018.05a
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• pp.83-84
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• 2018

전장 cDNA 클론을 시퀀싱하는 것은 선택적 스플라이싱 형태를 비롯한 정확한 유전자 구조를 정의하는데 유용하게 사용될 수 있으며, 유전자 및 단백질의 생물학적 기능연구에 중요한 자원을 제공한다. 포괄적이며 비 중복적인 cDNA의 생산은 인간 유전체 연구의 중요한 목표이다. 본 연구에서 제공하는 인간 cDNA 라이브러리 분석 파이프라인은 전장 cDNA를 분석하는 자동화 도구로 여러 연구자들에게 활용 될 수 있을 것으로 사료된다.

• Proceedings of the Korean Information Science Society Conference
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• 2004.04b
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• pp.340-342
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• 2004

Promsearch는 인간 DNA에서 코어 프로모터 영역을 예측하는 프로그램이며, PWM(position weight matrix)과 신경망을 기반으로 전사시작지점을 예측한다. 프로그램은 대량의 서열 데이터를 처리할 수 있도록 구성되었으며, 본 논문에서는 인간 염색체 22번에 대한 프로모터 예측 결과를 제시한다. Annotated된 936개의 유전자와 Promsearch가 예측한 프로모터간의 위치의 상관관계를 계산한 결과 87개에 대해 프로모터 예측 결과가 의미 있는 것으로 밝혀졌다. 예측의 민감도는 25%이며, Promsearch가 대규모 시퀀싱 프로젝트에서 나오는 대량의 서열 데이터를 1차적으로 분석하는 도구로서 사용될 수 있음을 확인하였다.

• Microbiology and Biotechnology Letters
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• v.44 no.1
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• pp.84-88
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• 2016

In this study, bacterial diversity in the living room and bathroom of a residential environment was analyzed using the pyrosequencing method. There was no difference in the diversity index of bacteria between the 2 rooms; however, differences were noted in the composition of bacteria. The classes ${\beta}$-Proteobacteria and ${\delta}$-Proteobacteria were found in the bathroom at higher abundances than in the living room. The phyla Acidobacteria, Chlorobi, Chloroflexi, Fusobacteria, Nitrospirae, and Planctomycetes were found in the bathroom, but not in the living room, indicating a broader range of bacteria. However, the living room showed a more diverse range of bacterial genera than the bathroom did. In both the living room and the bathroom, the genus Methylobacterium was dominant.