• Journal of Microbiology and Biotechnology
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• v.26 no.8
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• pp.1473-1480
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• 2016

This study focused on the variations in the non-coding sequences between ctxB and rstR of various CTX phages. The non-coding sequences of CTX-1 and CTX-cla are phage type-specific. The length of the non-coding region of CTX-1 and CTX-cla is 601 and 730 nucleotides, respectively. The non-coding sequence of CTX phage could be divided into three regions. There is a phage type-specific Variable region between two homologous Common regions (Common regions 1 and 2). The non-coding sequence of RS1 element is similar to CTX-1 except that Common region 1 is replaced by a short RS1-specific sequence. The non-coding sequences of CTX-2 and CTX-cla are homologous, indicating the non-coding sequence of CTX-2 is derived from CTX-cla. The non-coding region of CTX-O139 is similar to CTX-cla and CTX-2; however, it contains an extra phage type-specific sequence between Common region 2 and rstR. The variations in the non-coding sequences of CTX phages might be associated with the difference in the replication efficiency and the directionality in the integration into the V. cholerae chromosome.

• Biomedical Science Letters
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• v.24 no.3
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• pp.221-229
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• 2018

Trichophyton rubrum is one of the well-known pathogenic fungi and causes dermatophytosis and cutaneous mycosis in human world widely. However, there are not an available sequence type (ST) classification methods and previous studies for T. rubrum until now. Therefore, currently, molecular biological tools using their DNA sequences are used for genotype identification and classification. In the present study, in order to characterize the genetic diversity and the phylogenetic relation of T. rubrum clinical isolates, five different housekeeping genes, such as actin (ACT), calmodulin (CAL), RNA polymerase II (RPB2), superoxide dismutase 2 (SOD2), and ${\beta}$-tubulin (BT2) were analyzed using by multilocus sequence typing (MLST). Also, DNA sequence analysis was performed to examine the differences between the sequences of Trichophyton strains and the identified genetic variations sequence. As a result, most of the sequences were shown to have highly matched rates in their housekeeping genes. However, genetic variations were found on three different positions of ${\beta}$-tubulin gene and were shown to have changed from $C{\rightarrow}G$ (1766), $G{\rightarrow}T$ (1876), and $C{\rightarrow}A$ (1886). To confirm the association with T. rubrum inheritance, a phylogenetic tree analysis was performed. It was classified as four clusters, but there was little significant correlation. Even so, MLST analysis is believed to be helpful for determining the genetic variations of T. rubrum in cases where there is more large-scale data accumulation. In conclusion, the present study demonstrated the first MLST analysis of T. rubrum in Korea and explored the possibility that MLST could be a useful tool for studying the epidemiology and evolution of T. rubrum through further studies.

• KIISE Transactions on Computing Practices
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• v.21 no.3
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• pp.263-268
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• 2015

Malware variations could be defined as malicious executable files that have similar functions but different structures. In order to classify the variations, this paper analyzed sequence alignment, the method used in Bioinformatics. This method found common parts of the Malwares' API call information. This method's performance is dependent on the API call information's length; if the length is too long, the performance should be very poor. Therefore we removed the repeated patterns in API call information in order to improve the performance of sequence alignment analysis, before the method was applied. Finally the similarity between malware was analyzed using sequence alignment. The experimental results with the real malware samples were presented.

• Animal Systematics, Evolution and Diversity
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• v.27 no.1
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• pp.1-17
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• 2011

Thais Roding, 1798, commonly known as rock-shell, is among the most frequently found gastropod genera worldwide on intertidal rocky shores including those of Japan, China, Taiwan and Korea. This group contains important species in many marine environmental studies but species-level taxonomy of the group is quite complicated due to the morphological variations in shell characters. This study examined the genetic variations and relationships among three Korean Thais species based on the partial nucleotide sequences of mitochondrial cox1 gene fragments. Phylogenetic trees from different analytic methods (maximum parsimony, neighbor-joining, and maximum likelihood) showed that T. bronni and T. luteostoma are closely related, indicating the most recent common ancestry. The low sequence divergence found between T. luteostoma and T. bronni, ranging from 1.53% to 3.19%, also corroborates this idea. Further molecular survey using different molecular marker is required to fully understand a detailed picture of the origin for their low level of interspecific sequence divergence. Sequence comparisons among conspecific individuals revealed extensive sequence variations within the three species with maximum values of 2.43% in T. clavigera and 1.37% in both T. bronni and T. luteostoma. In addition, there is an unexpectedly high level of mitochondrial genotypic diversity within each of the three Korean Thais species. The high genetic diversity revealed in Korean Thais species is likely to reflect genetic diversity introduced from potential source populations with diverse geographic origins, such as Taiwan, Hong Kong, and a variety of different coastal regions in South China and Japan. Additional sequence analysis with comprehensive taxon sampling from unstudied potential source populations will be also needed to address the origin and key factors for the high level of genetic diversity discovered within the three Korean Thais species studied.

• Genomics & Informatics
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• v.6 no.4
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• pp.166-172
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• 2008

A multitude of protein-coding sequence variations (CVs) in the human genome have been revealed as a result of major initiatives, including the Human Variome Project, the 1000 Genomes Project, and the International Cancer Genome Consortium. This naturally has led to debate over how to accurately assess the functional consequences of CVs, because predicting the functional effects of CVs and their relevance to disease phenotypes is becoming increasingly important. This article surveys and compares variation databases and in silico prediction programs that assess the effects of CVs on protein function. We also introduce a combinatorial approach that uses machine learning algorithms to improve prediction performance.

• Honam Mathematical Journal
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• v.34 no.4
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• pp.533-548
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• 2012

We investigate relations of polynomials $x^n={\Sigma}^{n-1}_{i=0}x^i$ and recurrence sequences. We consider certain variations of the Fibonacci sequence and investigate explicit ways to compute the general nth term.

• Korean Journal of Medicinal Crop Science
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• v.18 no.3
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• pp.173-179
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• 2010

This study describes an efficient approach to the development of DNA markers for use in distinguishing the Scrophularia species that have been used as useful medicinal crops. In order to distinguish Scrophularia species, DNA sequences of rpl-5 region in mitochondrial DNA of Scrophularia species were analysed for detecting sequence variations, and the PCR-RFLP method was applied for developing practicable DNA marker patterns. Several DNA variations were detected by the sequence comparison of rpl-5 region among Scrophularia species. Genetic relationship analysis of Scrophularia species was carried out based on these DNA variations. DNA variations of rpl-5 region were revealed that it was significantly efficient in genetic relationship analysis of Scrophularia species. In addition, Scrophularia species tested in this study were completely discriminated by four polymorphic genotypes by PCR-RFLP combined with Tsp509 I (^AATT) restriction enzyme. Our results suggested that DNA sequence variations of rpl-5 region were sufficiently useful for genetic relationship analysis of Scrophularia species. Polymorphic genotypes by PCR-RFLP using the Tsp509 I enzyme will be useful for discrimination of Scrophularia species as a practicable DNA markers.

• Publications of The Korean Astronomical Society
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• v.15 no.spc1
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• pp.15-30
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• 2000

A large scatter of the chemical abundances among globular cluster red giants has been observed. Especially the chemical elements C, N, O, Na, Mg, and Al vary form star to star within globular clusters. Except for $\omega$ Cen and M22, most globular clusters could be considered to be monometallic of their iron peak elements within error ranges. The variations in light elements among globuar cluster giants appear much more pronounced than in field halo giants of comparable Fe-peak metallicity. It has been found that in general the nitrogen abundance is anticorrelated with both carbon and oxygen, while it is correlated with Na and AI. These intracluster abundance inhomogeneities can be interpreted either by mixing of nucleosythesized material from the deep stellar interior during the red giant branch phase of evolution or by inhomogeneities of primordially processed material, from which the stars were formed. The simple way of distingushing between two senarios is to obtain the element abundances of main-sequence stars in globular clusters, which are too faint for high resolution spectroscopic studies until now. Both 'evolutionary' and 'primodial' origins are accepted for explanations of abundance variations among red giants and CN-CH anticorrelations among main-sequence stars in globular clusters. This paper reviews chemical abundances of light elements among globular cluster giants, with brief reviews of cannonical stellar evolution of low mass stars after main-sequence and deep mixing for abundance variations of cluster giants, and a possible connection between deep mixing and second parameter.

• Phonetics and Speech Sciences
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• v.1 no.1
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• pp.63-67
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• 2009

In this paper, in order to protect music copyrights, we propose a music identification system which is scalable to the number of pieces of registered music and robust to signal-level variations of registered music. For its implementation, we define the new concepts of 'music word' and 'music phoneme' as recognition units to construct 'music acoustic models'. Then, with these concepts, we apply the HMM-based framework used in continuous speech recognition to identify the music. Each music file is transformed to a sequence of 39-dimensional vectors. This sequence of vectors is represented as ordered states with Gaussian mixtures. These ordered states are trained using Baum-Welch re-estimation method. Music files with a suspicious copyright are also transformed to a sequence of vectors. Then, the most probable music file is identified using Viterbi algorithm through the music identification network. We implemented a music identification system for 1,000 MP3 music files and tested this system with variations in terms of MP3 bit rate and music speed rate. Our proposed music identification system demonstrates robust performance to signal variations. In addition, scalability of this system is independent of the number of registered music files, since our system is based on HMM method.

• Proceedings of the KIPE Conference
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• 1998.07a
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• pp.388-394
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• 1998

In this paper, we propose a speed sensorless control of the saturated induction motor using the zero sequence third harmonic voltages and a compensation method of the stator resistance variations. The air-gap flux of the saturated induction motor contains the space harmonic components rorating synchronous frequency. As a function of the air-gap flux saturation, the dominant third harmonic voltage is used to compensate the non-linear variations of the mutual inductance depending on the saturation level of the motor. and also the stator resistance variations can be measured with the phase angle between the voltage vector and the zero sequencial voltages. The validity of the proposed compensation scheme in the speed sensorless control using rotor flux observer is verified by simulations.