• Genomics & Informatics
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• v.6 no.3
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• pp.157-159
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• 2008

Multiple sequence alignment (MSA) is the most important step for many of biological sequence analyses, homology search, and protein structural assignments. However, large amount of data make biologists difficult to perform MSA analyses and it requires much computational time to align many sequences. Here, we have developed a simple and fast web alignment tool for aligning, editing, and visualizing large amount of sequence data. We used a cluster server installed ClustalW-MPI using web services and message passing interface (MPI). It also enables users to edit multiple sequence alignments for manual editing and to download the input data and results such as alignments and phylogenetic tree.

• Journal of the Korea Institute of Information Security & Cryptology
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• v.16 no.1
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• pp.115-122
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• 2006

The most methods for intrusion detection are based on the misuse detection which accumulates hewn intrusion information and makes a decision of an attack against any behavior data. However it is very difficult to detect a new or modified aoack with only the collected patterns of attack behaviors. Therefore, if considering that the method of anomaly behavior detection actually has a high false detection rate, a new approach is required for very huge intrusion patterns based on sequence. The approach can improve a possibility for intrusion detection of known attacks as well as modified and unknown attacks in addition to the similarity measurement of intrusion patterns. This paper proposes a method which applies the multiple sequence alignments technique to the similarity matching of the sequence based intrusion patterns. It enables the statistical analysis of sequence patterns and can be implemented easily. Also, the method reduces the number of detection alerts and false detection for attacks according to the changes of a sequence size.

• Korean Journal of Microbiology
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• v.35 no.2
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• pp.115-120
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• 1999

Multiple Sequence Alignment of DNA and protem sequences is a imnport'mt tool in the study of molecular evolution, gene regulation. and prolein suucture-function relationships. Progressive pairwise alignment method generates multiple sequence alignment fast but not necessarily with optimal costs. Dynamic programming generates multiple sequence alig~~menl with optimal costs in most cases but long execution time. In this paper. we suggest genetlc algorithm lo improve the multiple sequence alignment generated from the cnlent methods, describe the design of the genetic algorithm, and compare the multiple sequence alignments from 0111 method and current methods.

• Journal of Microbiology and Biotechnology
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• v.11 no.4
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• pp.693-699
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• 2001

An intracellular levansucrase gene, lscR from Rahnella aquatilis ATCC 15552, was cloned and its nucleotide sequence was determined. Nucleotide sequence analysis of this gene revealed a 1,238 bp open reading frame coding for a protein of 415 amino acids. The levansucrase was expressed by using a T7 promoter in Escherichia coli BL21 (DE3) and the enzyme activity was detected in the cytoplasmic fraction. The optimum pH and temperature of this enzyme for levan formation was pH 6 and $30^{\circ}C$, respectively. The deduced amino acid sequence of the lscR gene showed a high sequence similarity (59-89%) with Gram-negative levansucrses, while the level of similarity with Gram-positive enzymes was less than 42%. Multiple alignments of levansucrase sequences reported from Gram-negative and Gram-positive bacteria revealed seven conserved regions. A comparison of the catalytic properties and deduced amino acid sequence of lscR with those of other bacterial levansucrases strongly suggest that Gram-negative and Gram-positive levansucrases have an overall different structure, but they have a similar structure at the active site.

• Genomics & Informatics
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• v.7 no.1
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• pp.46-48
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• 2009

Finishing is the most time-consuming step in sequencing, and many genome projects are left unfinished due to complex repeat regions. Here, we have developed BACContigEditor, a prototype shotgun sequence finishing tool. It is essentially an editor that visualizes assemblies of shotgun sequence fragment reads as gapped multiple alignments. The program offers some flexibility that is needed to rapidly resolve complex regions within a working session. The sole purpose of the release is to promote collaborative creation of extensible software for fragment assembly editors, foster collaborative development, and reduce barriers to initial tool development effort. We describe our software architecture and identify current challenges. The program is available under an Open Source license.

• BMB Reports
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• v.41 no.5
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• pp.394-399
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• 2008

Multiple sequence alignments of the Bombyx mori fibroin light chain gene (fib-L) from hybrids and from Chinese and Japanese strains demonstrated that 51.6% of the fib-L third intron is conserved. One of these conserved segments, 41 bp long, contains the sequence CGTTATTATACATATT, which is duplicated in the B. mori Nd-$s^D$ mutant. In the present work, electrophoretic mobility assays and computational analyses revealed a major peak of intrinsic bent DNA within the segment that undergoes breakage in the previously-described Nd-$s^D$ mutation. This result suggested that this intrinsically-curved region might mediate DNA cleavage and enhance recombination events in the third intron of the Bombyx mori fib-L gene.

• International Journal of Industrial Entomology and Biomaterials
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• v.10 no.1
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• pp.25-33
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• 2005

Recently a cDNA clone of apoLp-III from Hyphantria cunea was isolated and subjected to computational analysis to compare with other available sequences. Multiple sequence alignments were carried out using the amino acid sequences of apoLp-III from six insects. It was found that the H. cunea apoLp-III has relatively high sequence identities to Spodoptera litura ($69.5\%$), Manduca sexta ($66.8\%$), Galleria mellonella ($65.1\%$), Bombyx mori N4 ($54.3\%$) but less identity to Locusta migratoria ($18.3\%$). The amino acid composition was compared with other insects using EXPASY tools; it shows that alanine (Ala), glutamine (Gln), leucine (Leu) and lysine (Lys) are the major amino acid components of apoLp-III in H. cunea as well as other lepidopterans. Homology modeling performed using PSI-BLAST (PDB template M. sexta) reveals that the apoLp-III molecules consist of five, long amphipathic alpha helical bundles with short loops connecting the helices and shows homology with other insects. Phylogenetic analysis shows that the orthopteran apoLp-III represented by locust was most distantly related to the lepidopteran insects.

• Tuberculosis and Respiratory Diseases
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• v.81 no.3
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• pp.216-221
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• 2018

Background: The number of immigrants with tuberculosis (TB) increases each year in South Korea. Determining the transmission dynamics based on whole genome sequencing (WGS) to cluster the strains has been challenging. Methods: WGS, annotation refinement, and orthology assignment for the GenBank accession number acquisition were performed on two clinical isolates from Chinese immigrants. In addition, the genomes of the two isolates were compared with the genomes of Mycobacterium tuberculosis isolates, from two native Korean and five native Chinese individuals using a phylogenetic topology tree based on the Multiple Alignment of Conserved Genomic Sequence with Rearrangements (Mauve) package. Results: The newly assigned accession numbers for two clinical isolates were CP020381.2 (a Korean-Chinese from Yanbian Province) and CP022014.1 (a Chinese from Shandong Province), respectively. Mauve alignment classified all nine TB isolates into a discriminative collinear set with matched regions. The phylogenetic analysis revealed a rooted phylogenetic tree grouping the nine strains into two lineages: strains from Chinese individuals and strains from Korean individuals. Conclusion: Phylogenetic trees based on the Mauve alignments were supposed to be useful in revealing the dynamics of TB transmission from immigrants in South Korea, which can provide valuable information for scaling up the TB screening policy for immigrants.

• Genomics & Informatics
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• v.2 no.3
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• pp.142-146
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• 2004

Biological data and analysis tools are accumulated in distributed databases and web servers. For this reason, biologists who want to find information from the web should be aware of the various kinds of resources where it is located and how it is retrieved. Integrating the data from heterogeneous biological resources will enable biologists to discover new knowledge across the specific domain boundaries from sequences to expression, structure, and pathway. And inevitably biological databases contain noisy data. Therefore, consensus among databases will confirm the reliability of its contents. We have developed WeSAT that integrates distributed and heterogeneous biological databases and analysis tools, providing through Web Services protocols. In WeSAT, biologists are retrieved specific entries in SWISS-PROT/EMBL, PDB, and KEGG, which have annotated information about sequence, structure, and pathway. And further analysis is carried by integrated services for example homology search and multiple alignments. WeSAT makes it possible to retrieve real time updated data and analysis from the scattered databases in a single platform through Web Services.

• Research in Plant Disease
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• v.21 no.4
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• pp.341-345
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• 2015

Virus-like symptoms including stunt, severe mosaic with malformation of leaves, fern-like leaves and abnormal petals were observed from an African impatiens (Impatiens walleriana) grown in a plant nursery in Icheon, Korea. Serological analysis using immuno-strip kits for viruses reported in African impatiens indicated that Cucumber mosaic virus (named CMV-Im) was a causal agent for the symptomatic African impatiens. Biological properties of CMV-Im were analyzed using responses of host plant species, suggesting that CMV-Im is a typical strain that belongs to CMV subgroup I. RT-PCR analysis verified CMV-Im infection from naturally infected African impatiens or mechanically inoculated some host species. Analysis of multiple alignments of CMV capsid protein (CP) sequences showed that CMV-Im shared high CP amino acids identities with other CMV strains. Phylogenetic tree analysis for the CP sequences of CMV-Im and representative CMV strains confirmed that CMV is a typical member of CMV subgroup I. To our knowledge, it is the first report of CMV in African impatiens in Korea.