• Journal of the Korea Society of Computer and Information
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• v.14 no.1
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• pp.73-80
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• 2009

G protein-coupled receptors(GPCRs) family is a cell membrane protein, and plays an important role in a signaling mechanism which transmits external signals through cell membranes into cells. But, GPCRs each are known to have various complex control mechanisms and very unique signaling mechanisms. Structural features, and family and subfamily of GPCRs are well known by function. and accordingly, the most fundamental work in studies identifying the previous GPCRs is to classify the GPCRs with given protein sequences. Studies for classifying previously identified GPCRs more easily with mathematical models have been mainly going on. In this paper Considering that functions of proteins are determined by their stereoscopic structures, the present paper proposes a method to compare secondary structures of two GPCRs having different amino acid sequences, and then detect an unknown GPCRs assumed to have a same function in databases of previously identified GPCRs.

• The korean journal of orthodontics
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• v.33 no.3 s.98
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• pp.185-197
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• 2003

This study was performed to identify the characteristics of the OFC1 gene (locus: chromosome 6p24.3) in Korean patients, which is assumed to be the major gene behind the nonsyndromic cleft lip and palate. The sample consisted of 80 subjects: 40 nonsyndromic cleft lip and palate patients (proband, 20 males and females, mean age 14.2 years); and 40 normal adults (20 males and 20 females, mean age 25.6 years). Using PCR-based assay, the OFC1 gene was amplified, sequenced, and then searched for similar protein structures. Results were as follows: 1. The OFC1 gene contains the microsatellite marker 'CA' repeats. The number of the reference 'CA' repeats was 21 times, and formed as TA(CA)11TA(CA)10. But, in Koreans, the number of tandem 'CA' repeats was varied from 17 to 26 except 18, and 'CA' repeats consisted of TA(CA)n. 2. Nine allelic variants were found. Distribution of the OFC1 allele was similar between the patients and control group. 3. There was a replacement of the base 'T' to 'C' after 11 tandem 'CA' repeats in Koreans compared with Weissenbach's report. However, the difference did not seem to be the ORF prediction results between Koreans and Weissenbach's report. 4. The BLAST search results showed the Telomerase reverse transcriptase (TERT) and the Nucleotide binding protein 2 (NBP2) as similar proteins. The TERT was a protein product by the hTERT gene in the locus 5p15.33 (NCBI Genome Annotation; NT023089) The NBP2 was a protein product by the ABCC3 (ATP-binding cassette, sub-family C) gene in the locus 17q22 (NCBI Genome Annotation; NT010783). 5. In the Pedant-Pro database analysis, the predictable protein structure of the OFC1 gene had at least one transmembrane region and one non-globular region.

• Horticultural Science & Technology
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• v.35 no.3
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• pp.344-360
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• 2017

Zoysiagrasses are important turf plants used for school playgrounds, parks, golf courses, and sports fields. The two most popular zoysiagrass species are Zoysia japonica and Zoysia sinica. These are widely distributed across different growing zones and are morphologically distinguishable from each other; however, it is phenotypically difficult to differentiate those that grow along the coastal line from those in beach area habitats. A combination of morphological and molecular approaches is desirable to efficiently identify these two plant cultivars. In this study, we used a rapid identification system based on DNA barcoding of the nrDNA-internal transcribed spacer (ITS) regions. The nrDNA-ITS regions of ITS1, 5.8S nrDNA, and ITS2 from Z. japonica, Z. sinica, Agrostis stolonifera, and Poa pratensis were DNA barcoded to classify these grasses according to their molecular identities. The nrDNA-ITS sequences of these species were found at 686 bp, 687 bp, 683 bp, and 681 bp, respectively. The size of ITS1 ranged from 248 to 249 bp, while ITS2 ranged from 270 to 274 bp. The 5.8S coding region ranged from 163 - 164bp. Between Z. japonica and Z. sinica, nineteen (2.8%) nucleotide sites were variable, and the G+C content of the ITS region ranged from 55.4 to 63.3%. Substitutions and insert/deletion (indel) sites in the nrDNA-ITS sequence of Z. japonica and Z. sinica were converted to cleaved amplified polymorphic sequence (CAPS) markers, and applied to the Zoysia grasses sampled to verify the presence of these markers. Among the 62 control and collected grass samples, we classified three groups: 36 Z. japonica, 22 Z. sinica, and 4 Z. japonica/Z. sinica hybrids. Morphological classification revealed only two groups; Z. japonica and Z. sinica. Our results suggest that used of the nrDNA-ITS barcode region and CAPS markers can be used to distinguish between Z. japonica and Z. sinica at the species level.

• Korean Journal of Breeding Science
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• v.42 no.5
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• pp.547-554
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• 2010

Low-molecular-weight glutenin subunit (LMW-GS) in common wheat (Triticum aestivum L.) is important for quality processing of bread and noodles. The objectives of this study were to clarify the composition of LMW-GSs and to identify their corresponding proteins. Using LMW-GS specific primers we cloned and characterized 43 LMW-GS genes in the wheat cultivar 'Jokyoung'. Some of these genes contain polypeptides different in size due to the presence of various deletions or insertions within repetitive and glutamine-rich domains. The comparison of deduced amino acid sequence of the LMW-GS genes in Jokyoung with that of 12 groups LMW-GSs of wheat cultivar Norin 61 showed that the deduced amino acid sequences were nearly the same to LMW-GS groups of 1, 2, 3/4, 5, 7, 10 and 11. All LMW-GS genes contain eight cysteine residues, which are conserved among all of the typical LMW-GS sequences. The relative positions of cysteine residues are also conserved, except those of the first and seventh. Based on phylogenetic analysis, the 43 sequences with the same N-terminal and C-terminal amino acid sequences were clustered in the same group. To identify the proteins containing the corresponding amino acid sequences, we determined the N-terminal amino acid sequence of 7 spots of LMW-GSs of Jokyoung separated by two-dimensional gel electrophoresis (2DE). Of them, Glu-B3 (LMW-m and LMW-s) and Glu-D3 (LMW-m) were detected in two and three spots, respectively and the others were not clear. Collectively, we classified diverse LMW-GSs and identified their corresponding protein products. These results will be helpful in breeding programs for improvement of wheat flour quality.

• The KIPS Transactions:PartC
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• v.10C no.2
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• pp.119-124
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• 2003

Although there have been many studies on using finite automata for intrusion detection, it has been a difficult problem to generate compact finite automata automatically. In a previous research an approach to profile normal behaviors using finite automata was proposed. They divided the system call sequence of each process into three parts prefix, main portion, and suffix, and then substituted macros for frequently occurring substrings. However, the procedure was not automatic. In this paper we present algorithms to automatically generate intrusion detection automata from the sequence of system calls resulting from the normal runs of the programs. We also show the effectiveness of the proposed method through experiments.

• The Journal of the Institute of Internet, Broadcasting and Communication
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• v.9 no.2
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• pp.29-36
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• 2009

Due to the progress of Bioinformatics field, We are making use of analyzing tools for effective analyzing enormous data of DNA sequence. But there was inconvenience in existing tools when searching and applying data for analyzing. Our treatise proposes a tool developed by a form based on RIA(Rich Internet Application) that you can solve the problems came from weak points. The analyzing tool for RIA indexing data of DNA sequence shows the results by real time in basis of Web 2.0 which supplemented basis on a form of Web. The web application was developed in Flex2 on Windows workstation.

• Korean Journal of Agricultural Science
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• v.36 no.2
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• pp.159-165
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• 2009

This study was conducted to identify the PERV (Porcine Endogenous Retrovirus) integration sites and their characterizations using the porcine genomic sequence information. Total 114 Mb (4.2%) sequence of the 2.7 Gb pig genome was investigated for the PERV sequences. As the results, 8 PERV sequences were identified and their genomic structures were deduced from the BLAST searches against previously known PERV genes. Seven PERVs have internal deletions in the protein coding region and they will not be functional. The other one also has internal deletions in the gag and env genes, indicating this PERV is also defective. Even though we could not identify the functional PERVs in this study, the results presented here can be used for the fundamental research materials for controlling PERV infections in relation to xenotransplantation using porcine organs and tissues.

• Korean journal of applied entomology
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• v.46 no.1 s.145
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• pp.169-173
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• 2007

Root-knot nematode damage was found on yam, Dioscorea bulbifera in Andong Korea. From the root-knots, female nematodes were isolated and subjected to DNA sequence analysis. Sequence of cytochrome oxidase subunit II (COII) was analyzed from the genomic DNA of the isolate. COII locus size and sequence of the nematode isolate were similar to those of Meloidogyne javanica or M. incognita. However, an analysis of HinfI restriction site, a species-specific character between these two species, showed that the isolate did not match to either M. javanica or M. incognita.

• Animal Systematics, Evolution and Diversity
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• v.19 no.2
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• pp.297-304
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• 2003

Phylogenetic analysis of 31 species representing 12 genera in the family Strigidae (Aves: Strigiformes) including 5 species (Bubo bubo, Otus sunia, O. semitorques, Ninox scutulato, Strix aluco) collected from Korea has been undertaken using nucleotide sequences of the mitochondrial cytochrome b gene. Maximum likelihood analysis was performed and pairwise genetic distances were calculated with Kimura's two-parameter and p-distance. Among well-aligned 959 bp used for this study, 459 sites were variable and 398 sites were informative for the phylogenetic analysis. The family Strigidae was divided into three subgroups, Clade I (Aegolius), Clade II (Athene, Micrathene, Glaucidium and Surnia) and Clade III (Bubo, Nycteo, Pulsatrix, Strix, Otus, Ptilopsis, and Ninox). Also, two separated subgroups in the genus Otus were confirmed by the geographical distribution.

• Journal of KIISE
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• v.43 no.3
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• pp.289-295
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• 2016

Malware authors spread malware variants in order to evade detection. It's hard to detect malware variants using static analysis. Therefore dynamic analysis based on API call information is necessary. In this paper, we proposed a malware family recommendation method to assist malware analysts in classifying malware variants. Our proposed method extract API call information of malware families by dynamic analysis. Then the multiple sequence alignment technique was applied to the extracted API call information. A signature of each family was extracted from the alignment results. By the similarity of the extracted signatures, our proposed method recommends three family candidates for unknown malware. We also measured the accuracy of our proposed method in an experiment using real malware samples.