• Interdisciplinary Bio Central
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• v.6 no.4
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• pp.3.1-3.10
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• 2014

Amino acid substitution matrices are essential tools for protein sequence analysis, homology sequence search in protein databases and multiple sequence alignment. The PAM matrix was the first widely used amino acid substitution matrix. The BLOSUM series then succeeded the PAM matrix. Most substitution matrixes were developed by using the statistical frequency of substitution between each amino acid at blocks representing groups of protein families or related proteins. However, substitution of amino acids is based on the similarity of physiochemical properties of each amino acid. In this study, a new approach was used to obtain major physiochemical properties in multiple sequence alignment. Frequency of amino acid substitution in multiple sequence alignment database and selected attributes of amino acids in physiochemical properties database were merged. This merged data showed the major physiochemical properties through principle components analysis. Using factor analysis, these four principle components were interpreted as flexibility of electronic movement, polarity, negative charge and structural flexibility. Applying these four components, BAPS was constructed and validated for accuracy. When comparing receiver operated characteristic ($ROC_{50}$) values, BAPS scored slightly lower than BLOSUM and PAM. However, when evaluating for accuracy by comparing results from multiple sequence alignment with the structural alignment results of two test data sets with known three-dimensional structure in the homologous structure alignment database, the result of the test for BAPS was comparatively equivalent or better than results for prior matrices including PAM, Gonnet, Identity and Genetic code matrix.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2002.05a
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• pp.81-86
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• 2002

In current CBR(Case-Based Reasoning) systems, the case adaptation is usually performed by rule-based method that use rules hand-coded by the system developer. So, CBR system designer faces knowledge acquisition bottleneck similar to those found in traditional expert system design. In this thesis, 1 present a model for learning method of case adaptation knowledge using case base. The feature difference of each pair of cases are noted and become the antecedent part of an adaptation rule, the differences between the solutions in the compared cases become the consequent part of the rule. However, the number of rules that can possibly be discovered using a learning algorithm is enormous. The first method for finding cases to compare uses a syntactic measure of the distance between cases. The threshold fur identification of candidates for comparison is fixed th the maximum number of differences between the target and retrived case from all retrievals. The second method is to use similarity metric since the threshold method may not be an accurate measure. I suggest the elimination method of duplicate rules. In the elimination process, a confidence value is assigned to each rule based on its frequency. The learned adaptation rules is applied in riven target Problem. The basic. process involves search for all rules that handle at least one difference followed by a combination process in which complete solutions are built.

• Plant Biotechnology Reports
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• v.4 no.2
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• pp.165-172
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• 2010

Genes that are expressed early in specific response to high salinity conditions were isolated from rapeseed plant (Brassica napus L.) using an mRNA differential display method. Five PCR fragments (DD1.5) were isolated that were induced by, but showed different response kinetics to, 200 mM NaCl. Nucleotide sequence analysis and homology search revealed that the deduced amino sequences of three of the five cDNA fragments showed considerable similarity to those of ${\beta}$-mannosidase (DD1), tomato Pti-6 proteins (DD5), and the tobacco harpin-induced protein hin1 (DD4), respectively. In contrast, the remaining clones, DD3 and DD2, did not correspond to any substantial existing annotation. Using the DD3 fragment as a probe, we isolated a full-length cDNA clone from the cDNA library, which we termed BnSWD1 (Brassica napus salt responsive WD40 1). The predicted amino-acid sequence of BnSWD1 contains eight WD40 repeats and is conserved in all eukaryotes. Notably, the BnSWD1 gene is expressed at high levels under salt-stress conditions. Furthermore, we found that BnSWD1 was upregulated after treatment with abscisic acid, salicylic acid, and methyl jasmonate. Our study suggests that BnSWD1, which is a novel WD40 repeat-containing protein, has a function in salt-stress responses in plants, possibly via abscisic acid-dependent and/or -independent signaling pathways.

• Journal of the Korea Computer Industry Society
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• v.5 no.9
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• pp.859-872
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• 2004

With the rapid advance of computer and communication techonology, the recent trend of education environment is edveloping in the ubiquitous learning (u-learning) direction that learners select and organize the contents, time and order of learning by themselves. Since the amount of education information through the internet is increasing rapidly and it is managed in document in an effective way is necessary. The document clustering is integrated documents to subject by classifying a set of documents through their similarity among them. Accordingly, the document clustering can be used in exploring and searching a document and it can increased accuracy of search. This paper proposes an efficient incremental clustering method for a set of documents increase gradually. The incremental document clustering algorithm assigns a set of new documents to the legacy clusters which have been identified in advance. In addition, to improve the correctness of the clustering, removing the stop words can be proposed.

• Parasites, Hosts and Diseases
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• v.44 no.4 s.140
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• pp.331-341
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• 2006

Actin binding proteins play key roles in cell structure and movement particularly as regulators of the assembly, stability and localization of actin filaments in the cytoplasm. In the present study, a cDNA clone encoding an actin bundling protein named as AhABP was isolated from Acanthamoeba healyi, a causative agent of granulomatous amebic encephalitis. This clone exhibited high similarity with genes of Physarum polycephalum and Dictyostelium discoideum, which encode actin bundling proteins. Domain search analysis revealed the presence of essential conserved regions, i.e., an active actin binding site and 2 putative calcium binding EF-hands. Transfected amoeba cells demonstrated that AhABP is primarily localized in phagocytic cups, peripheral edges, pseudopods, and in cortical cytoplasm where actins are most abundant. Moreover, AhABP after the deletion of essential regions formed ellipsoidal inclusions within transfected cells. High-speed co-sedimentation assays revealed that AhABP directly interacted with actin in the presence of up to $10{\mu}M$ of calcium. Under the electron microscope, thick parallel bundles were formed by full length AhABP, in contrast to the thin actin bundles formed by constructs with deletion sites. In the light of these results, we conclude that AhABP is a novel actin bundling protein that is importantly associated with actin filaments in the cytoplasm.

• Ocean and Polar Research
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• v.28 no.2
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• pp.107-117
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• 2006

Freshwater algal studies in North polar environments are relatively few. This study presented the algal-flora, -biomass and genetic features of dominant cells collected from temporary ponds around the Polar Research Station (PRS), Norway. Water samples were collected from 4 stations around PRS, and analyzed for their environmental and biological variables. Water temperature, salinity and conductivity ranged from 5 to $10^{\circ}C$, 0.1 to $0.3%_{\circ}$ and 0.21 to $0.36{\mu}S/cm$, respectively. Chlorophyll a concentration ranged from 1.8 to $11.1{\mu}g/l$, and that of the size-fractionated cells was recorded from 0.7 to $1.1{\mu}g/l$ in picoplankton 0.3 to $6.5{\mu}g/l$ in nanoplankton, and 0.4 to $3.9{\mu}g/l$ in microplankton respectively. Algal flora in the present study was recorded as 10 genera, in which Chlamydomonas, particularly, was dominant in all studied sites. By comparison of Chlamydomonas 18S rDNA sequences, including two isolates from PRS, they formed a distinct clade against others: sequence similarity was significantly low (<97.2%) with C. noctigama, being the highest score by BLAST search in GenBank. This study was valuable for basic knowledge regarding the freshwater algae around PRS and their genetic information.

• Journal of Korea Multimedia Society
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• v.2 no.4
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• pp.409-418
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• 1999

The fractal image compression is based on the self-similarity that some area in an image exhibits a very similar shape with other areas. This compression technique has very long encoding time although it has high compression ratio and fast decompression. To cut-off the encoding time, most researches have restricted the search of domain blocks for a range block. These researches have been mainly focused on the coherence between a domain block and a range block, while they have not utilized the coherence among range blocks well. Therefore, we give an analysis on the coherence among range blocks in order to develope an efficient fractal Image compression algorithm. We analysis the range blocks according to not only measures for defining the range block coherence but also threshold of each measure. If these results are joined in a prior work of other fractal compression algorithms, it will give a great effectiveness in encoding time.

• Journal of KIISE
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• v.41 no.10
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• pp.838-846
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• 2014

Three-dimensional (3D) object retrieval from user-drawn sketch queries is one of the important research issues in the areas of pattern recognition and computer graphics for simulation, visualization, and Computer Aided Design. The performance of content-based 3D object retrieval system depends on the availability of effective descriptors and similarity measures for this kind of data. In this paper, we present a sketch-based 3D object retrieval system by extracting a hybrid edge descriptor which is robust against rotation and translation. The experimental results which are based on HTML5 and WebGL show that proposed sketch-based 3D object retrieval method is very efficient to search and order the 3D objects according to user's intention.

• Journal of the Korea Institute of Information Security & Cryptology
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• v.26 no.2
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• pp.405-413
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• 2016

In this paper, we propose a proactive inference method of finding suspicious domains. Our method detects potential malicious domains from the seed domain information extracted from the TLD Zone files and WHOIS information. The inference process follows the three steps: searching the candidate domains, machine learning, and generating a suspicious domain pool. In the first step, we search the TLD Zone files and build a candidate domain set which has the same name server information with the seed domain. The next step clusters the candidate domains by the similarity of the WHOIS information. The final step in the inference process finds the seed domain's cluster, and make the cluster as a suspicious domain set. In experiments, we used .COM and .NET TLD Zone files, and tested 10 seed domains selected by our analysts. The experimental results show that our proposed method finds 55 suspicious domains and 52 true positives. F1 scores 0.91, and precision is 0.95 We hope our proposal will contribute to the further proactive malicious domain blacklisting research.

• Journal of KIISE:Computing Practices and Letters
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• v.6 no.3
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• pp.288-298
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• 2000

Digital assets denote multimedia information that exists in the form of digitized materials such as images, audio, and video. The management of digital assets demands much effort because of a huge amount of storage space requirement and multidimensional characteristics of the information needed to describe their contents. In this paper, we design and implement a Digital Asset Manager that stores and manages digital assets efficiently. Among the various types of digital assets, we focus on the video asset which has the highest complexity. Our Digital Asset Manager provides various facilities for digital contents authoring applications. In the Digital Asset Manager, video assets are managed by using a hierarchical model in order to ensure efficient accesses to any part of a video asset. Our system also guarantees the independence from the storage platform, and provides a fast content-based similarity search method on the digital assets.