• Korean Journal of Microbiology
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• v.44 no.4
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• pp.333-338
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• 2008

Computational analysis of partial rpoB gene sequence (777 bp) was done in this study to identify B. anthracis and its closely related species B. cereus and B. thuringiensis. Sequence data including 17 B. anthracis strains, 9 B. cereus strains, and 7 B. thuringiensis strains were obtained by searching databases. Those sequences were aligned and used for other computational analysis. B. anthracis strains were identificated by in silico restriction enzyme digestion. B. cereus and B. thuringiensis were not segregated by this method. Those sequencing and BLAST search were required to distinguish the two. In actual identification tests, B. anthracis strains could be identified by PCR-RFLP, and B. cereus and B. thuringiensis strains were distinguished by BLAST search with reliable e-value. In this study fast and accurate method for identifying three Bacillus species, and flow chart of identification were developed.

• Journal of the Korea Society of Computer and Information
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• v.14 no.2
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• pp.139-147
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• 2009

BLAST (Basic Local Alignment Search Tool) is a best well-known tool in a bioinformatics area. BLAST quickly compares input sequences with annotated huge sequence databases and predicts their functions. It helps biologists to make it easy to annotate newly found sequences with reduced experimental time, scope, and cost. However, as the amount of sequences is increasing remarkably with the advance of sequencing machines, performance of BLAST has been a critical issue and tried to solve it with several alternatives. In this paper, we propose a new PC-Based Cluster system (E-Cluster), a new physical data design methodology (logical partitioning technique) and a query routing technique (intra-query routing). To verify our system, we measure response time, speedup, and efficiency for various sizes of sequences in NR (Non-Redundancy) database. Experimental result shows that proposed system has better speedup and efficiency (maximum 600%) than those o( conventional approaches such as SMF machines, clusters, and grids.

• Proceedings of the Zoological Society Korea Conference
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• 2001.04a
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• pp.52.1-52
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• 2001

No Abstract, See Full Text

• Korean Journal of Microbiology
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• v.38 no.4
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• pp.267-275
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• 2002

We have developed GComp as an analysis tool for microbial genome comparison. This tool exploits BLAST or FASTA as a preprocessing program for local alignments to detect homologous regions, 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. Our test cases shows that the program can be useful in practice for intuitive and quantitative comparison of microbial genome sequence pairs as well as self-genome analysis. A few additional features have been devised and designed, which will be added in the further development.

• Journal of Crop Science and Biotechnology
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• v.10 no.4
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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.

• Journal of Institute of Control, Robotics and Systems
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• v.11 no.10
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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

• Biomedical Science Letters
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• v.10 no.4
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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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• v.4 no.4
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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.

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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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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• 2011.11a
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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.