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서열 및 상호작용 정보를 활용한 이종간 유사 기능 단백질 추출
설영주(Young-Joo Seol),김민경(Min Kyung Kim),유성준(Seong-Joon Yoo),박선희(Seon Hee Park) 한국정보과학회 2004 한국정보과학회 학술발표논문집 Vol.31 No.2Ⅱ
단백질 간 상호작용은 생물체 내에서 발생하는 모든 생명 현상을 이루는 기본 단위로써, 이를 종 수준에서 밝히고자 하는 시도가 yeast와 초파리, worm등에서 보고되었다. 대량으로 존재하는 상호작용 데이터들은 종래에 서열로 시도되던 유연관계 비교 및 기능 유추 등에 기본 정보로 활용되고 있다. 본 연구에서는 다른 중에 속하는 동일 기능 단백질 즉 ortholog를 찾음에 있어 기존의 서열 접근 방식 이외에 상호작용 정보를 추가로 사용하는 시스템을 고안하여 서열방식만을 활용하던 이전의 방식이 지니는 문제점을 극복하고자 하였다.
Transcriptomics Analyses of Genes Regulating Anthocyanin Production in Black Rice
이재희,설영주,한장호,원소윤,Yong-Jae Won,김용갑,김용환,김병기,김창국 한국바이오칩학회 2015 BioChip Journal Vol.9 No.1
We used a 135K rice microarray to identifygenes involved in anthocyanin biosynthesis andmetabolism in black rice. Using our multi-interactionscreening method, we then screened 427 expressiongenes, 754 orthologous genes, and 416 pathway-networkrelated genes associated with anthocyanin biosynthesis. Finally, we identified eight candidate genesby comparing pathway-expression genes, includingortholog-ontology genes. To verify the candidate genes,each was mapped to the black rice genome, and functionalpredictions were confirmed via phylogeneticreconstructions using the candidate genes and theirhomologous proteins. While the eight genes identifiedby our method require further characterization andvalidation, our study demonstrates the power of multiinteractionscreening after the initial identification ofgenes with microarrays.
An Information-based Model for an Interactive Web Service with Agricultural Biotechnology
김창국,설영주,박동석,한장호 한국유전체학회 2011 Genomics & informatics Vol.9 No.2
The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a biological informationbased database. The major functions of the NABIC are focused on biotechnological developments for agricultural bioinformatics and providing a web-based service to construct bioinformatics workflows easily, such as protein function prediction and genome systems biology programs. The NABIC has concentrated on the functional genomics of major crops, building an integrated biotechnology database for agro-biotech information that focuses on the proteomics of major agricultural resources,such as rice, Chinese cabbage, rice Ds-tagging lines, and microorganisms.
김민경,설영주,박현석,장승환,신항철,조광휘 한국유전체학회 2009 Genomics & informatics Vol.7 No.3
Developed proteome-scale ortholog and paralog prediction methods are mainly based on sequence similarity. However, it is known that even the closest BLAST hit often does not mean the closest neighbor. For this reason, we added conserved interaction information to find orthologs. We propose a genome-scale, automated ortholog prediction method, named OrthoInterBlast. The method is based on both sequence and interaction similarity. When we applied this method to fly and yeast, 17% of the ortholog candidates were different compared with the results of Inparanoid. By adding protein-protein interaction information, proteins that have low sequence similarity still can be selected as orthologs, which can not be easily detected by sequence homology alone.
박태호,진미나,이상춘,홍준기,설영주,문정환,박범석 한국원예학회 2011 Horticulture, Environment, and Biotechnology Vol.52 No.3
Glutathione S-transferases (GSTs) have medically and agriculturally important roles in plants such as herbicide detoxification, responses to biotic and abiotic stress and catalytic reaction of anticancer compounds. The fully sequenced Arabidopsis thaliana and rice (Oryza sativa) genome revealed identification of 52 and 61 members of GSTs, and 28 and 39 of those belong to the Tau class of GSTs (GSTUs), respectively. Based on the sequences of AtGSTUs, 14 BAC clones derived from Brassica rapa that contain similar sequences of AtGSTUs were identified and 17 unique sequences of open reading frames were detected in the 14 BAC clones using blast search and sequence alignment. Those sequences were designated the Tau class candidate of GST derived from B. rapa (BrGSTUs) and it is confirmed that BrGSTUs are also clustered in tandem as it has been known to be common feature in plant. They were mapped on BrR5, BrR7, BrR8, BrR9, or BrR10, and their nucleotide and amino acid sequences were highly similar to those of AtGSTUs. In addition, in silico analysis of BrGSTUs was performed using Korea Brassica Genome Project 24 K (KBGP-24K) oligochip and microarray database for cold, salt, and drought stresses. The results of this study will facilitate further researches for breeding of Chinese cabbage containing medically and agriculturally important traits.
조민석,이장하,허남한,김창국,설영주,한장호,백지현,김홍기,박동석 한국미생물학회 2012 The journal of microbiology Vol.50 No.3
The Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis is the causal agent of canker disease in tomato. Because it is very important to control newly introduced inoculum sources from commercial materials, the specific detection of this pathogen in seeds and seedlings is essential for effective disease control. In this study, a novel and efficient assay for the detection and quantitation of C. michiganensis subsp. michiganensis in symptomless tomato and red pepper seeds was developed. A pair of polymerase chain reaction (PCR) primers (Cmm141F/R) was designed to amplify a specific 141 bp fragment on the basis of a ferredoxin reductase gene of C. michiganensis subsp. michiganensis NCPPB 382. The specificity of the primer set was evaluated using purified DNA from 16 isolates of five C. michiganensis subspecies, one other Clavibacter species, and 17 other reference bacteria. The primer set amplified a single band of expected size from the genomic DNA obtained from the C. michiganensis subsp. michiganensis strains but not from the other C. michiganensis subspecies or from other Clavibacter species. The detection limit was a single cloned copy of the ferredoxin reductase gene of C. michiganensis subsp. michiganensis. In conclusion, this quantitative direct PCR assay can be applied as a practical diagnostic method for epidemiological research and the sanitary management of seeds and seedlings with a low level or latent infection of C. michiganensis subsp. michiganensis.
백정호,김도완,오재현,이동준,설영주,김창국,김준아,백정현,이홍로,이태호 한국정보과학회 2015 데이타베이스 연구 Vol.31 No.2
With the advent of genome sequencing era, various bioinformatics tools have been developed to analyze the genomes. The estimation of evolutionary pressure via Synonymous substitutions rate (Ks) and the Nonsynonymous substitutions rate (Ka) in protein-coding regions broadly used is essential for the comparative analysis. However, most of analysis tools are composed of command line interface (CLI)-based multi-step method and cause difficulties to computer-illiterate biologists. So, we introduce the ToolbKx (Toolbox Ka and Ks, web-based selective pressure analysis system) to perform the genome analysis handily. Core programs such as calculating the Ka and Ks values are implemented by Python and BASH scripts. The results are shown to users by data visualization framework on the web. CLI-based complex analysis can be progressed via web with ease and it is convenient that researcher can perform the comparative analysis of genomes by providing the results in graph format. 유전체 시대의 도래와 함께 다수의 유전체를 효율적으로 비교 및 분석하기 위해 다양한 생명정보학 도구들이 개발 되어 왔다. 그 중 유전자 서열비교를 통해 단백질 코딩영역에서 Synonymous substitution 비율(Ks)과 Nonsynonymous substitution 비율(Ka) 측정 및 이들을 이용한 선택압 종류 예측은 Command Line Interface (CLI)를 가진 다수의 프로그램을 순차적으로 이용하는 형태로 이루어져 왔으며 이러한 형태의 분석방법은 컴퓨터에 익숙하지 않은 많은 생물학자들에게 많은 어려움과 불편함을 주었다. 본 연구팀은 이러한 비교유전체 분석을 연구자들이 쉽고 편리하게 수행할 수 있도록 하기 위해 웹기반 선택압 분석지원 시스템(ToolbKx: Toolbox Ka and Ks)을 개발, 구축하였다. Ka, Ks 값 측정 등 분석을 담당하는 ToolbKx의 코어 프로그램은 Python, BASH 스크립트 등을 이용하여 구현되었으며 분석 결과는 웹상에서 데이터 시각화 프레임워크를 통해 사용자에게 보여 진다. CLI 기반의 복잡한 분석을 웹을 통해 쉽게 진행할 수 있고 분석 결과가 그래프 등을 통해 제공됨으로서 연구하는 사용자들의 유전체 비교, 분석 연구가 더욱 편리해질 것이다.