• 미생물학회지
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• 제44권4호
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• pp.333-338
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• 2008

Bacillus anthracis, B. cereus, B. thuringiensis 를 분류하기 위해 rpoB 유전자 배열을 이용한 컴퓨터 분석 작업을 수행하였다. 17개의 B. anthracis, 9개의 B. cereus, 7개의 B. thuringiensis 를 database에서 구하였다. B. anthracis 는 rpoB 유전자의 in silico 제한효소 절단에 의해, B. cereus, B. thuringiensis 2 group과 구별되었다. 그러나 B. cereus와 B. thuringiensis 는 제한효소 절단에 의해 구분되지는 않고, 염기배열과 Blast 탐색의 도움으로 구분이 가능하였다. 본 연구를 통해 3 종류의 Bacillus 종을 동정할 수 있는 알고리즘이 개발되었다.

• 한국컴퓨터정보학회논문지
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• 제14권2호
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• pp.139-147
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• 2009

BLAST는 생명정보학 분야에서 가장 많이 사용하는 도구이다. 이 도구는 입력서열을 기존 서열 데이터베이스와 신속히 비교하고 그 기능을 예측한다. 생물학자는 BLAST를 이용하여 실험의 범위, 시간과 비용을 줄일 수 있다. 하지만, 서열 데이터 양이 급격히 증가함에 따라 그 처리 시간도 같이 증가하여 성능개선 방안이 필요하다. 본 논문에서는 대용량 BLAST처리 성능 향상을 위한 PC 기반의 클러스터 인프라 (E-Cluster)를 제시하고 이 기반에서 데이터베이스 분할기법 (Logical Partitioning)과 질의 라우팅 기법(Intra-Query)을 제안한다. 제안된 시스템을 평가하기 위해 다양한 길이의 서열들과 NR 데이터베이스와 비교하여 응답시간(Response Time), 성능 향상(Speedup), 효율(Efficiency) 관점에서 평가한다. 본 실험을 통해 기존 SMP, Cluster, 그리드 기반의 BLAST 시스템보다 성능, 효율이 뛰어남을 확인하였고, 특히 제안한 시스템의 최대 효율은 600%로 매우 높았다.

• 한국동물학회:학술대회논문집
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• 한국동물학회 2001년도 공동 춘계학술대회
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• pp.52.1-52
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• 2001

No Abstract, See Full Text

• 미생물학회지
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• 제38권4호
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• pp.267-275
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• 2002

미생물 유전체 프로젝트의 결과인 유전체 서열에 대해, 비교 유전체 분석을 수행할 수 있는 분석 도구인 GComp를 개발하였다. 이 도구는 국부 상동성 계산을 BLAST나 FASTA를 사용하여 수행한 후에 그 결과를 받아들여, 상동성을 보이는 부분을 분석하고 위치 파악 및 연결한 뒤, 두 유전체간의 상동성 정도를 일목요연하게 보여줄 수 있는 테이블과 파일들을 생성한다. 한편. 그 결과를 그래픽으로 표시하고 전체를 살펴볼 수 있는 인터페이스 기능을 구현하였다. 시험 데이터로 기존의 미생물 유전체 서열을 상대로 분석하면서, 유전체 서열의 핵산 및 단백질 수준에서의 비교분석 결과를 통해 두 유전체에 대한 비교 정보를 효과적으로 확인할 수 있었고, 보다 다양한 분석을 위한 도구 개발의 기준을 설정할 수 있었다.

• Journal of Crop Science and Biotechnology
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• 제10권4호
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• pp.231-236
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• 2007

Differentially expressed genes(DEG) were identified in a rice variety, Sathi, an indica type showing high allelopathic potential against barnyardgrass(Echinochloa crus-galli(L.) Beauv. var. frumentaceae). Rice plants were grown with and without barnyardgrass and total RNA was extracted from rice leaves at 45 days after seeding. DEG full-screening was performed by $GeneFishing^{TM}$ method. The differentially expressed bands were re-amplified and sequenced, then analyzed by Basic Local Alignment Search Tool(BLAST) searching for homology sequence identification. Gel electrophoresis showed nine possible genes associated with allelopathic potential in Sathi, six genes(namely DEG-1, 4, 5, 7, 8, and 9) showed higher expression, and three genes(DEG-2, 3 and 6) showed lower expression as compared to the control. cDNA sequence analysis showed that DEG-7 and DEG-9 had the same sequence. From RT PCR results, DEG-6 and DEG-7 were considered as true DEG, whereas DEG-1, 2, 3, 4, 5, and 8 were considered as putative DEG. Results from blast-n and blast-x search suggested that DEG-1 is homologous to a gene for S-adenosylmethionine synthetase, DEG-2 is homologous to a chloroplast gene for ribulose 1,5-bisphosphate carboxylase large subunit, DEG-8 is homologous to oxysterol-binding protein with an 85.7% sequence similarity, DEG-5 is homologous to histone 2B protein with a 47.9% sequence similarity, DEG-6 is homologous to nicotineamine aminotransferase with a 33.1% sequence similarity, DEG-3 has 98.8% similarity with nucleotides sequence that has 33.1% similarity with oxygen evolving complex protein in photosystem II, DEG-7 is homologous to nucleotides sequence that may relate with putative serin/threonine protein kinase and putative transposable element, and DEG-4 has 98.8% similarity with nucleotides sequence for an unknown protein.

• 제어로봇시스템학회논문지
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• 제11권10호
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• pp.851-856
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• 2005

The DNA and protein data of diverse species have been daily discovered and deposited in the public archives according to each established format. Database systems in the public archives provide not only an easy-to-use, flexible interface to the public, but also in silico analysis tools of unidentified sequence data. Of such in silico analysis tools, multiple sequence alignment [1] methods relying on pairwise alignment and Smith-Waterman algorithm [2] enable us to identify unknown DNA, protein sequences or phylogenetic relation among several species. However, in the existing multiple alignment method as the number of sequences increases, the runtime increases exponentially. In order to remedy this problem, we adopted a parallel processing suffix tree algorithm that is able to search for common subsequences at one time without pairwise alignment. Also, the cross-matching subsequences triggering inexact-matching among the searched common subsequences might be produced. So, the cross-matching masking process was suggested in this paper. To identify the function of the clusters generated by suffix tree clustering, BLAST was combined with a clustering tool. Our clustering and annotating tool is summarized as the following steps: (1) construction of suffix tree; (2) masking of cross-matching pairs; (3) clustering of gene sequences and (4) annotating gene clusters by BLAST search. The system was successfully evaluated with 22 gene sequences in the pyrubate pathway of bacteria, clustering 7 clusters and finding out representative common subsequences of each cluster

• 대한의생명과학회지
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• 제10권4호
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• pp.523-528
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• 2004

The core factor of the study is integrated environment based PC-Cluster system and high speed access rate up to 155 Mbps, continuous collection system for bioinformatics information at home and abroad. The results of the study are establishment and stabilization of information and communication infrastructure, establishment and stabilization of high performance computer network up to 155 Mbps, development of PC-Cluster system with 32 nodes, a parallelized BLAST on Cluster system, which can provides scalable speedup in terms of response time, and development of collection and search system for bioinformatics information.

• Genomics & Informatics
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• 제4권4호
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• pp.167-169
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• 2006

PABAP (Palindrome Analysis by BLAST Program) is an analysis system that identifies palindromic sequences from a large genome sequence up to several megabases long. It uses NCBI BLAST as a searching engine, and data processing such as alignment filtration and detection of inverted repeats which satisfy user-defined parameters is performed by manipulating data after populating into a MySQL database. PABAP outperforms publicly available palindrome search program in that it can detect large palindrome with internal spacer at a faster speed from bacterial genomes. It is a standalone application and is freely available for noncommercial users.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2002년도 추계학술대회
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• pp.185-193
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• 2002

We have developed GComp as an analysis tool for comparative analysis of microbial genomes. Thetool uses BLAST or FASTA as a preprocessing program for local alignments, parses the homology search results, and generates tables and files to show homology relationship between two genomes at a glance. The interface for graphical representation of the comparative genomic analysis has been also implemented. Through analysis of a few pairs of microbial genome sequences, the program has been proved to be practically useful and a few additional features have been devised and designed, which will be added in the further development.

• 한국신재생에너지학회:학술대회논문집
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• 한국신재생에너지학회 2011년도 추계학술대회 초록집
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• pp.125.1-125.1
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• 2011

$CO_2$ separation from a flue gas by using the gas hydrate technology was suggested by Kang et al. They reported phase equilibrium conditions of mixed gases composed of $CO_2$ and N2 with THF as a thermodynamic promoter. In this study, we reported the phase equilibrium conditions of a mixed gas which had a realistic composition of the blast furnace gas (BFG) emitted from the steel-making process. The phase equilibrium measurements were done by using the "continuous" QCM method, and the results demonstrate that this method is efficient and as accurate as the conventional temperature search method.