• 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

• International Journal of Fuzzy Logic and Intelligent Systems
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• v.3 no.2
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• pp.222-226
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• 2003

Information retrieval must be able to search the most suitable document that user need from document set. If foretell document adaptedness by similarity degree about QL(Query Language) of document, documents that search person does not require are searched. In this paper, showed that can search the most suitable document on user's request searching document of the whole space using genetic algorithm and used knowledge-base operator to solve various model's problem.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 1995.10b
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• pp.98-103
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• 1995

In this paper, a method is presented for finding an optimal temperature control pattern in microwaveoven using genetic algorithm. Power spectrum of temperature variance of charcoal is obtained and oven system modeling with fuzzy-neural-network is explained. Fan on/off timing is converted to strings in gene pool and then genetic iterations make the power spectrum of simmulated temperature variance of microwave oven closer to that o charcoal.

• Computers and Concrete
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• v.27 no.1
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• pp.63-71
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• 2021

In this study, a new stopping criterion, called "backward controlled stopping criterion" (BCSC), was proposed to be used in Genetic Algorithms. In the study, the available stopping citeria; adaptive stopping citerion, evolution time, fitness threshold, fitness convergence, population convergence, gene convergence, and developed stopping criterion were applied to the following four comparison problems; high strength concrete mix design, pre-stressed precast concrete beam, travelling salesman and reinforced concrete deep beam problems. When completed the analysis, the developed stopping criterion was found to be more accomplished than available criteria, and was able to research a much larger area in the space design supplying higher fitness values.

• Journal of the Korean Institute of Intelligent Systems
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• v.14 no.5
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• pp.630-634
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• 2004

According to the progress of an information-oriented society, more human friendly systems are required. The systems can be implemented by a kind of intelligent algorithms. In this paper we propose the possibility of the implementation of an intelligent algorithm from gene, behavior of human beings, which has some properties such as self organization and self regulation. The regulation of gene behavior is widely analyzed by Boolean network. Also the SORE (Self Organizable and Regulating Engine) is one of those algorithms. This paper does not report detailed research results; rather, it studies the feasibility of gene behavior in biocontrol systems based upon computer simulations.

• The Korean Journal of Applied Statistics
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• v.24 no.4
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• pp.609-622
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• 2011

The pattern of methylation draws significant attention from cancer researchers because it is believed that DNA methylation and gene expression have a causal relationship. As the interest in the role of methylation patterns in cancer studies (especially drug resistant cancers) increases, many studies have been done investigating the association between gene expression and methylation. However, a model-based approach is still in urgent need. We developed a finite mixture model in the Bayesian framework to find a possible relationship between gene expression and methylation. For inference, we employ Expectation-Maximization(EM) algorithm to deal with latent (unobserved) variable, producing estimates of parameters in the model. Then we validated our model through simulation study and then applied the method to real data: wild type and hydroxytamoxifen(OHT) resistant MCF7 breast cancer cell lines.

• 한국데이터정보과학회:학술대회논문집
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• 2006.04a
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• pp.63-76
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• 2006

Several clustering algorithms to analyze gene expression data and cluster validation techniques that assess the quality of their outcomes, have been suggested, but evaluations of these cluster validation techniques have seldom been implemented. In this paper we compared various cluster validity indices for simulation data and real genomic data, and found that Dunn's index is more effective and robust through small simulations and with real gene expression data.

• Journal of Microbiology and Biotechnology
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• v.19 no.3
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• pp.323-330
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• 2009

Nontuberculous mycobacteria (NTM) are a major cause of opportunistic infections in immunocompromised patients, making the reliable and rapid identification of NTM to the species level very important for the treatment of such patients. Therefore, this study evaluated the usefulness of the novel target genes tuf and tmRNA for the identification of NTM to the species level, using a PCRrestriction fragment length polymorphism analysis (PRA). A total of 44 reference strains and 17 clinical isolates of the genus Mycobacterium were used. The 741 bp or 744 bp tuf genes were amplified, restricted with two restriction enzymes (HaeIII/MboI), and sequenced. The tuf gene-PRA patterns were compared with those for the tmRNA (AvaII), hsp65 (HaeIII/HphI), rpoB (MspI/HaeIII), and 16S rRNA (HaeIII) genes. For the reference strains, the tuf gene-PRA yielded 43 HaeIII patterns, of which 35 (81.4%) showed unique patterns on the species level, whereas the tmRNA, hsp65, rpoB, and 16S rRNA-PRAs only showed 10 (23.3%), 32 (74.4%), 19 (44.2%), and 3 (7%) unique patterns after single digestion, respectively. The tuf gene-PRA produced a clear distinction between closely related NTM species, such as M. abscessus (557-84-58) and M. chelonae (477-84-80-58), and M. kansasii (141-136-80-63-58-54-51) and M. gastri (141-136-117-80-58-51). No difference was observed between the tuf-PRA patterns for the reference strains and clinical isolates. Thus, a diagnostic algorithm using a tuf gene-targeting PRA is a promising tool with more advantages than the previously used hsp65, rpoB, and 16S rRNA genes for the identification of NTM to the species level.

• Journal of Korean Society for Quality Management
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• v.28 no.1
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• pp.13-26
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• 2000

It is really hard for the material factors to basically improve quality of life, since it is the only partial means of the survival and activity of life. Development of Eigen Shin-Tou-Jil(Proper Body·Earth materials), therefore, must be concentrated on providing man with essential meaning of life, not with simply economic advantage. Eigen Shin-Tou-Jil(Proper Body·Earth materials) which is formed through long passage of time in the original environments that include the climate and nature features of a special region, the representative examples are like Korea Bong-sam(a kind of genseng) of Yellow Earth etc. Unfolding the Eigen Shin-Tou-Jil(Proper Body·Earth materials) by the Algorithm of Human-ware means the development for manifesting individual eigen motives and traits as subject of behavior(Gene-ware). It is because all plants, animals, inanimate objects, including Human, have evolved with their own values in the ecosystem. It was reported that a Baeksong(white pine tree), grown well up in TongEeDong, Seoul, Korea had rarely grown up during the period suppressed by Japan. By the developments of Bio-Engineering, we also found that 40% of gene base sequence of C. Elegance(a kind of worm) is identical to that of characteristic Human. In this reason, through considering common characteristics between Human and Nature, the developments of Eigen Shin-Tou-Jil(Proper Body·Earth materials) must begin with epoch for manifesting and understanding individual's Eigen motives and traits as subject of behavior(Gene-ware)

• Journal of the Korean Data and Information Science Society
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• v.21 no.6
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• pp.1271-1280
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• 2010

We have used multifactor dimensionality reduction (MDR) method to study genegene interaction effect of statistical model in general. But, MDR method could not be applied in the continuous data. In this paper, continuous-type data by the support vector machine (SVM) algorithm are proposed to the MDR method which provides an introduction to the technique. Also we apply the method on the identify major interaction effects of single nucleotide polymorphisms (SNPs) responsible for economic traits in a Korean cattle population.