• 한국컴퓨터정보학회논문지
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• 제11권6호
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• pp.69-78
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• 2006

생물정보학 연구 있어서 아미노산이나 염기서열에 대한 유사성이나 상동성을 찾아내는 작업은 유전자의 기능에 대한 예측이나 단백질 구조를 예측하는 연구의 기반이 된다. 이러한 서열 데이터는 컴퓨터의 도입으로 매우 빠르게 증가하고 있다. 이러한 시점에서 서열에 대한 검색 속도는 매우 중요한 요소이기 때문에 대량의 서열정보를 다루기 위해서는 SMP(Sysmmetric Multi-Processors) 컴퓨터나 클러스터를 이용하고 있다. 본 논문에서는 서열 검색에 사용되는 BLAST(Basic Local Alignment Search Tool)의 속도향상을 위한 방법으로 클러스터 환경에서 병렬화 하는 nBLAST 알고리즘의 병렬화에 대해 제안한다. nBLAST는 기존의 BLAST 소스코드에 대한 수정 없이 병렬라이브러리인 MPI(Message Passing Interface)를 이용하여 질의를 분할하여 병렬화 하기 때문에 환경설정 등의 복잡한 과정을 거치지 않고 손쉽게 BLAST에 알고리즘에 대한 병렬화를 할 수 있다. 또한, 실험을 통하여 28대의 리눅스 클러스터에서 nBLAST를 수행하여 노드 수의 증가에 따른 성능 향상을 확인하였다.

• Genomics & Informatics
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• 제20권3호
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• pp.36.1-36.6
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• 2022

BLAST, a basic bioinformatics tool for searching local sequence similarity, has been one of the most widely used bioinformatics programs since its introduction in 1990. Users generally use the web-based NCBI-BLAST program for BLAST analysis. However, users with large sequence data are often faced with a problem of upload size limitation while using the web-based BLAST program. This proves inconvenient as scientists often want to run BLAST on their own data, such as transcriptome or whole genome sequences. To overcome this issue, we developed NBLAST, a graphical user interface-based BLAST program that employs a two-way system, allowing the use of input sequences either as "query" or "target" in the BLAST analysis. NBLAST is also equipped with a dot plot viewer, thus allowing researchers to create custom database for BLAST and run a dot plot similarity analysis within a single program. It is available to access to the NBLAST with http://nbitglobal.com/nblast.

• Structural Engineering and Mechanics
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• 제77권5호
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• pp.613-626
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• 2021

In this paper, an enhanced Violation-based Sensitivity analysis and Border-Line Adaptive Sliding Technique (ViS-BLAST) will be utilized for optimization of some well-known structural and mechanical engineering problems. ViS-BLAST has already been introduced by the authors for solving truss optimization problems. For those problems, this method showed a satisfactory enactment both in speed and efficiency. The Enriched ViS-BLAST or EVB is introduced to be vastly applicable to any solvable constrained optimization problem without any specific initialization. It uses one-directional step-wise searching technique and mostly limits exploration to the vicinity of FNF border and does not explore the entire design space. It first enters the feasible region very quickly and keeps the feasibility of solutions. For doing this important, EVB groups variables for specifying the desired searching directions in order to moving toward best solutions out or inside feasible domains. EVB was employed for solving seven numerical engineering design problems. Results show that for problems with tiny or even complex feasible regions with a larger number of highly non-linear constraints, EVB has a better performance compared to some records in the literature. This dominance was evaluated in terms of the feasibility of solutions, the quality of optimum objective values found and the total number of function evaluations performed.

• 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.

• 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.

• Journal of Microbiology and Biotechnology
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• 제22권8호
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• pp.1054-1058
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• 2012

In order to predict biologically significant attributes such as function from protein sequences, searching against large databases for homologous proteins is a common practice. In particular, BLAST and HMMER are widely used in a variety of biological fields. However, sequence-homologous proteins determined by BLAST and proteins having the same domains predicted by HMMER are not always functionally equivalent, even though their sequences are aligning with high similarity. Thus, accurate assignment of functionally equivalent proteins from aligned sequences remains a challenge in bioinformatics. We have developed the FEP-BH algorithm to predict functionally equivalent proteins from protein-protein pairs identified by BLAST and from protein-domain pairs predicted by HMMER. When examined against domain classes of the Pfam-A seed database, FEP-BH showed 71.53% accuracy, whereas BLAST and HMMER were 57.72% and 36.62%, respectively. We expect that the FEP-BH algorithm will be effective in predicting functionally equivalent proteins from BLAST and HMMER outputs and will also suit biologists who want to search out functionally equivalent proteins from among sequence-homologous proteins.

• 한국패류학회지
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• 제20권2호
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• pp.165-169
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• 2004

본 연구를 통해서 http://chimp.kribb.re kr/mollusks 에 연체동물 전용 서열 BLAST 데이터베이스가 구축되었다. 예비실험을 통해 본 결과와 마찬가지로 연체동물을 대상으로 한 유전자 정보만을 매우 빠른 속도로 얻을 수 있었다. 본 시스템을 사용하여 앞으로 많은 연구가 진행되어질 연체동물 유전자 연구 및 EST 연구에 많은 도움이 되리라고 사료된다.

• 제어로봇시스템학회논문지
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• 제12권10호
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• pp.1044-1049
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• 2006

Multiple sequence alignment is a method to compare two or more DNA or protein sequences. Most of multiple sequence alignment tools rely on pairwise alignment and Smith-Waterman algorithm to generate an alignment hierarchy. Therefore, 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 and CDD (Conserved Domain Database)search were combined with a clustering tool. Our clustering and annotating tool consists of constructing suffix tree, overlapping common subsequences, clustering gene sequences and annotating gene clusters by BLAST and CDD search. The system was successfully evaluated with 36 gene sequences in the pentose phosphate pathway, clustering 10 clusters, finding out representative common subsequences, and finally identifying functional domains by searching CDD database.

• 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.

• The Plant Pathology Journal
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• 제26권3호
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• pp.280-285
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• 2010

In the course of a searching natural antifungal compounds from plant sources, we found that the methanol extract ($3,000\;{\mu}g/ml$) of Malus domestica fruits had potential of control against rice blast (Magnaporthe grisea) and tomato late blight (Phytophthora infestans). Under bioassay-guided purification, we isolated phloretin, a phenolic compound, with in vivo antifungal activity against M. grisea. By 1-day protective application of phloretin ($500\;{\mu}g/ml$), the compound strongly inhibited the disease development of M. grisea and P. infestans on rice and tomato seedlings, respectively. And red pepper anthracnose caused by Colletotrichum coccodes also was moderately suppressed. However, rice sheath blight (Rhizoctonia solani AG1), and barley powdery mildew (Blumeria graminis f. sp. hordei) were hardly controlled. In addition, the compound showed in vitro antifungal activity against some plant pathogenic fungi including Phytophthora capsici, Alternaria panax, Sclerotinia sclerotiorum, R. solani AG4, and M. grisea. This is the first report on the antifungal activity of phloretin against plant pathogenic fungi.