• 융합신호처리학회논문지
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• 제7권1호
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• pp.11-16
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• 2006

To manipulate large video databases, effective video indexing and retrieval are required. A large number of video indexing and retrieval algorithms have been presented for frame-w]so user query or video content query whereas a relatively few video sequence matching algorithms have been proposed for video sequence query. In this paper, we propose an efficient algorithm to extract key frames using color histograms and to match the video sequences using edge features. To effectively match video sequences with low computational load, we make use of the key frames extracted by the cumulative measure and the distance between key frames, and compare two sets of key frames using the modified Hausdorff distance. Experimental results with several real sequences show that the proposed video retrieval algorithm using color and edge features yields the higher accuracy and performance than conventional methods such as histogram difference, Euclidean metric, Battachaya distance, and directed divergence methods.

• 한국컴퓨터산업학회논문지
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• 제4권4호
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• pp.613-624
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• 2003

본 논문은 우선순위 큐와 접미어 트리로 색인 구조를 생성한 후. 이미지 시퀀스 데이터베이스에서 다차원 타임 워핑 거리 함수를 이용하여 유사한 이미지 서브시퀀스를 신속하고 정확하게 검색할 수 있는 방법을 제안한다. 본 논문에서 제안된 방법은 사전에 정의된 중요도에 따라 선별된 이미지 시퀀스로 구성된 우선순위 큐 색인의 이미지 서브시퀀스에 대한 유사성 거리 계산을 첫 단계로 시행하여 유사한 서브시퀀스집합을 얻고 만족할 결과를 얻지 못했을 경우에는 두 번째 단계로 나머지 유사 서브시퀀스에 대해 디스크 기반의 접미어 트리를 색인 구조체로 하여 유사한 서브시퀀스를 검색하는 것이다. 하한 거리 함수를 활용하여 질의 이미지 시퀀스와 유사한 이미지 서브시퀀스를 검색하는 과정에서 생성 가능한 오류를 방지 하면서 동시에 비 유사 이미지 서브시퀀스를 제거하도록 한다.

• Journal of Microbiology and Biotechnology
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• 제9권4호
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• pp.404-413
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• 1999

Methanopyrus kandleri is a hyperthermophilic methanogen that represents one of the most heat-resistant organisms: the maximum growth temperature of M. kandleri is $110^{\circ}C$. A random sequence analysis of the genomic DNA of M. kandleri has been performed to obtain genomic information. More than 200 unique sequence tags were obtained and compared with the sequences in the GenBank and PIR databases. About 30% of the analyzed tags showed strong sequence similarity to previously identified genes involved in various cellular processes such as biosynthesis, transport, methanogenesis, or metabolism. When statistics relating to the frequency of codons were examined, the sequenced open reading frames showed highly biased codon usage and a high content of charged amino acids. Among the identified genes, a homologue of the catalytic subunit of carbon monoxide dehydrogenase (CODH) that reduces $CO_2$ to CO was cloned and sequenced in order to examine its detailed gene structure. The cloned gene includes consensus promoters. The amino acid sequence of the cloned gene shows a strong homology with the CODH genes from methanogenic Archaea, especially in the presumed binding sites for Fe-S centers.

• Journal of Microbiology and Biotechnology
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• 제17권8호
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• pp.1330-1337
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• 2007

To better understand the gene expression of the cold-adapted polar diatom, we conducted a survey of the Chaetoceros neogracile transcriptome by cDNA sequencing and expression of interested cDNAs from the Antarctic diatom. A non-normalized cDNA library was constructed from the C. neogracile, and a total of 2,500 cDNAs were sequenced to generate 1,881 high-quality expressed sequence tags (ESTs) (accession numbers EL620615-EL622495). Based on their clustering, we identified 154 unique clusters comprising 342 ESTs. The remaining 1,540 ESTs did not cluster. The number of unique genes identified in the data set is thus estimated to be 1,694. Taking advantage of various tools and databases, putative functions were assigned to 939 (55.4%) of these genes. Of the remaining 540 (31.9%) unknown sequences, 215 (12.7%) appeared to be C. neogracile-specific since they lacked any significant sequence similarity to any sequence available in the public databases. C. neogracile consisted of a relatively high percentage of genes involved in metabolism, genetic information processing, cellular processes, defense or stress resistance, photosynthesis, structure, and signal transduction. From the ESTs, the expression of these putative C. neogracile genes was investigated: fucoxanthin chlorophyll (chl) a,c-binding protein (FCP), ascorbate peroxidase (ASP), and heat-shock protein 90 (HSP90). The abundance of ASP and HSP90 changed substantially in response to different culture conditions, indicating the possible regulation of these genes in C. neogracile.

• 정보처리학회논문지D
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• 제10D권4호
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• pp.577-590
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• 2003

모양 기반 검색이란 실제 요소 값과 관계없이 질의 시퀀스와 유사한 모양을 갖는 시퀀스(서브시퀀스)를 데이터베이스 내에서 검색하여 내는 연산이다. 본 논문에서는 시계열 데이터베이스에서의 모양 기반 검색을 위한 유연성 있는 새로운 유사 모델을 정의하고, 이 유사 모델을 지원하기 위한 인덱싱 및 질의 처리 방안을 제시한다. 제안된 유사 모델에서는 정규화, 이동 평균, 타임 워핑 등 다양한 변환을 지원한다. 특히 최종 유사 정도를 계산하기 위하여 사용되는$L_p$거리 함수론 사용자가 임의로 지정하도록 함으로써 응용에서 선호하는 유사 모델을 반영할 수 있다. 또한 이러한 모양 기반 검색을 효과적으로 지원하기 위한 압축된 서브시퀀스 트리 구조를 제안하고, 이를 기반으로 하는 효율적인 질의 처리 기법을 제시한다. 실험 결과에 의하면 제안된 기법은 진의 시퀀스와 모양이 유사한 서브시퀀스들을 사용자에 의하여 선택된 거리 함수를 사용하여 성공적으로 검색할 뿐 아니라, 순차 검색과 비교하여 거리 함수 선택에 따라 수 십배에서 수 백배까지의 성능 개선 효과를 갖는 것으로 나타났다.

• 정보처리학회논문지D
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• 제11D권5호
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• pp.1003-1010
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• 2004

본 논문에서는 시계열 데이터베이스에서 서브시퀀스 매칭을 효과적으로 처리하는 방안에 관하여 논의한다. 먼저, 본 논문에서는 서브시퀀스 매칭을 위한 기존 기법의 인덱스 검색에서 발생하는 성능상의 문제점들을 지적하고, 이들을 해결할 수 있는 새로운 방법을 제시한다. 제안된 기법은 서브시퀀스 매칭의 인덱스 검색 문제를 윈도우-조인이라는 일종의 공간 조인 문제로 새롭게 해석하는 것에서 출발한다. 윈도우-조인의 빠른 처리를 위하여 제안된 기법에서는 서브시퀀스 매칭을 시작할 때 질의 시퀀스를 위한 R＊-트리를 주기억장치 내에 구성한다. 또한, 제안된 기법은 데이터 시퀀스들을 위한 디스크 상의 R＊-트리와 질의 시퀀스를 위한 주기억장치 상의 R＊-트리를 효과적으로 조인할 수 있는 새로운 알고리즘을 포함한다. 이 알고리즘은 데이터 시퀀스들을 위한 R＊-트리 페이지들을 인덱스 단계의 착오 채택 없이 단 한번만 디스크로부터 액세스하므로 디스크 액세스 측면에서 최적의 기법임이 증명된다. 또한, 다양한 실험을 통한 성능 평가를 통하여 제안된 기법의 우수성을 정량적으로 규명한다.

• Journal of the Korean Wood Science and Technology
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• 제18권2호
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• pp.49-66
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• 1990

In order to identify an unknown wood sample native to Korea. the softwood databases(KSWCHUN; Korean SoftWood CHUN) and the hardwood databases(KHWCHUN; Korean HardWood CHUN) had been built. and the new computer searching programs(IDINEX; IDentification INformation EXpress) has been written in Turbo Pascal(V.5.0) and in Macro Assembly(V.5.0). The characters of the data were based on the 74 features of softwood and on the 148 features of hardwood which are a part of new "IAWA list of microscopic features for hardwood identification" published in 1989. For the purpose of this investigation the wood anatomical nature of 25 species of softwood(13 genera of 5 families) and of 112 species of hardwood(57 genera of 31 families) were observed under a scanning electron microscope and light microscope. and a lot of literature used. The IDINEX programs are based on edge-punched card keys. with several improvements. The maximum number of features in the IDINEX is 229. but that is fixed for a given database. Large numbers of taxa are handled efficiently and new taxa easily added. A search may be based on sequence numbers of features. Comparisons are made sequentially by feature and taxon using the entire suite of features specified to produce the list of possible matching taxa. The results are followings. (1) The databases of Korean wood and the searching programs(IDINEX) had been built. (2) The databases of Korean wood could be an information to search an unknown wood. (3) The databases would be valuable. for the new features, which were not mentioned in Korean wood up to the present. were observed in details. (4) The ultrastructures of the cell walls(warty layer) and crystals observed under a scanning electron microscope will be helpful to search an unknown wood in particular. (5) The searching process is more quick and accurate than the others. 6) We can obtain the information on the differences of a species from the other and search an unknown wood using probability. in IDINEX, (7) The IDINEX will be utilized to identify and classify an animal life, vegetable world, mineral kingdom, and so on.

• Journal of Microbiology and Biotechnology
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• 제30권9호
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• pp.1335-1342
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• 2020

The identification of bacterial pathogens to humans is critical for environmental microbial risk assessment. However, current methods for identifying pathogens in environmental samples are limited in their ability to detect highly diverse bacterial communities and accurately differentiate pathogens from commensal bacteria. In the present study, we suggest an improved approach using a combination of identification results obtained from multiple databases, including the multilocus sequence typing (MLST) database, virulence factor database (VFDB), and pathosystems resource integration center (PATRIC) databases to resolve current challenges. By integrating the identification results from multiple databases, potential bacterial pathogens in metagenomes were identified and classified into eight different groups. Based on the distribution of genes in each group, we proposed an equation to calculate the metagenomic pathogen identification index (MPII) of each metagenome based on the weighted abundance of identified sequences in each database. We found that the accuracy of pathogen identification was improved by using combinations of multiple databases compared to that of individual databases. When the approach was applied to environmental metagenomes, metagenomes associated with activated sludge were estimated with higher MPII than other environments (i.e., drinking water, ocean water, ocean sediment, and freshwater sediment). The calculated MPII values were statistically distinguishable among different environments (p < 0.05). These results demonstrate that the suggested approach allows more for more accurate identification of the pathogens associated with metagenomes.

• Journal of Microbiology and Biotechnology
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• 제24권10호
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• pp.1301-1307
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• 2014

White-rot fungi of the genus Bjerkandera are cosmopolitan and have shown potential for industrial application and bioremediation. When distinguishing morphological characters are no longer present (e.g., cultures or dried specimen fragments), characterizing true sequences of Bjerkandera is crucial for accurate identification and application of the species. To build a framework for molecular identification of Bjerkandera, we carefully identified specimens of B. adusta and B. fumosa from Korea based on morphological characters, followed by sequencing the internal transcribed spacer region and 28S nuclear ribosomal large subunit. The phylogenetic analysis of Korean Bjerkandera specimens showed clear genetic differentiation between the two species. Using this phylogeny as a framework, we examined the identification accuracy of sequences available in GenBank. Analyses revealed that many Bjerkandera sequences in the database are either misidentified or unidentified. This study provides robust reference sequences for sequence-based identification of Bjerkandera, and further demonstrates the presence and dangers of incorrect sequences in GenBank.

• 대한원격탐사학회:학술대회논문집
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• 대한원격탐사학회 2004년도 Proceedings of ISRS 2004
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• pp.99-102
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• 2004

Recently according to developing of bioinformatics techniques, there are a lot of researches about large amount of biological data. And a variety of files and databases are being used to manage these data efficiently. However, because of the deficiency of standardization there are a lot of problems to manage the data and transform one into the other among heterogeneous formats. We are interested in integrating. saving, and managing gene and protein sequence data generated through sequencing. Accordingly, in this paper the goal of our research is to implement the system to manage sequence data and transform a sequence file format into other format. To satisfy these requirements, we adopt BSML (Bioinformatics Sequence Markup Language) as the standard to manage the bioinformatics data. And then we integrate and store the heterogeneous 리at file formats using BSML schema based DTD. And we developed the system to apply the characteristics of object-oriented database and to process XPath query, one of the efficient structural query. that saves and manages XML documents easily.