• Genomics & Informatics
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• v.21 no.2
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• pp.21.1-21.14
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• 2023

Fusobacterium nucleatum is a gram-negative bacteria associated with diverse infections like appendicitis and colorectal cancer. It mainly attacks the epithelial cells in the oral cavity and throat of the infected individual. It has a single circular genome of 2.7 Mb. Many proteins in F. nucleatum genome are listed as "Uncharacterized." Annotation of these proteins is crucial for obtaining new facts about the pathogen and deciphering the gene regulation, functions, and pathways along with discovery of novel target proteins. In the light of new genomic information, an armoury of bioinformatic tools were used for predicting the physicochemical parameters, domain and motif search, pattern search, and localization of the uncharacterized proteins. The programs such as receiver operating characteristics determine the efficacy of the databases that have been employed for prediction of different parameters at 83.6%. Functions were successfully assigned to 46 uncharacterized proteins which included enzymes, transporter proteins, membrane proteins, binding proteins, etc. Apart from the function prediction, the proteins were also subjected to string analysis to reveal the interacting partners. The annotated proteins were also put through homology-based structure prediction and modeling using Swiss PDB and Phyre2 servers. Two probable virulent factors were also identified which could be investigated further for potential drug-related studies. The assigning of functions to uncharacterized proteins has shown that some of these proteins are important for cell survival inside the host and can act as effective drug targets.

• Proceedings of the Korean Society for Language and Information Conference
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• 2007.11a
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• pp.405-414
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• 2007

This paper describes a preliminary work on prosody modeling aspect of a text-to-speech system for Thai. Specifically, the model is designed to predict symbolic markers from text (i.e., prosodic phrase boundaries, accent, and intonation boundaries), and then using these markers to generate pitch, intensity, and durational patterns for the synthesis module of the system. In this paper, a novel method for annotating the prosodic structure of Thai sentences based on dependency representation of syntax is presented. The goal of the annotation process is to predict from text the rhythm of the input sentence when spoken according to its intended meaning. The encoding of the prosodic structure is established by minimizing speech disrhythmy while maintaining the congruency with syntax. That is, each word in the sentence is assigned a prosodic feature called strength dynamic which is based on the dependency representation of syntax. The strength dynamics assigned are then used to obtain rhythmic groupings in terms of a phonological unit called foot. Finally, the foot structure is used to predict the durational pattern of the input sentence. The aforementioned process has been tested on a set of ambiguous sentences, which represents various structural ambiguities involving five types of compounds in Thai.

• International Journal of Contents
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• v.2 no.1
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• pp.22-28
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• 2006

In this paper, we propose new semantic contents modeling using individual features, associative relations and visual features for efficiently supporting browsing and retrieval of video semantic contents. And we implement and design a browsing and retrieval system based on the semantic contents modeling. The browsing system supports annotation based information, keyframe based visual information, associative relations, and text based semantic information using a tree based browsing technique. The retrieval system supports text based retrieval, visual feature and associative relations according to the retrieval types of semantic contents.

• Journal of Microbiology and Biotechnology
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• v.22 no.6
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• pp.788-792
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• 2012

We report the computational structural simulation of the Cry1Ab19 toxin molecule from B. thuringiensis BtX-2 based on the structure of Cry1Aa1 deduced by x-ray diffraction. Validation results showed that 93.5% of modeled residues are folded in a favorable orientation with a total energy Z-score of -8.32, and the constructed model has an RMSD of only $1.13{\AA}$. The major differences in the presented model are longer loop lengths and shortened sheet components. The overall result supports the hierarchical three-domain structural hypothesis of Cry toxins and will help in better understanding the structural variation within the Cry toxin family along with facilitating the design of domain-swapping experiments aimed at improving the toxicity of native toxins.

• Journal of KIISE:Computing Practices and Letters
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• v.7 no.5
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• pp.510-521
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• 2001

Image retrieval system should be construct for searching fast, efficient image be extract the accurate feature information of image with more massive and more complex characteristics. Image retrieval system are essential differences between image databases and traditional databases. These differences lead to interesting new issues in searching of image, data modeling. So, cause us to consider new generation method of database, efficient retrieval method of image. In this paper, To extract feature information of edge using in searching from input image, we was performed to extract the edge by convolution Laplacian mask and input image, and we implemented the annotation-based and content-based image retrieval system for searching fast, efficient image by generation image database from extracting feature information of edge and metadata. We can improve the performance of the image contents retrieval, because the annotation-based and content-based image retrieval system is using image index which is made up of the content-based edge feature extract information represented in the low level of image and annotation-based edge feature information represented in the high level of image. As a conclusion, image retrieval system proposed in this paper is possible the accurate management of the accumulated information for the image contents and the information sharing and reuse of image because the proposed method do construct the image database by metadata.

• Genomics & Informatics
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• v.18 no.3
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• pp.28.1-28.9
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• 2020

Streptomyces coelicolor is a gram-positive soil bacterium which is well known for the production of several antibiotics used in various biotechnological applications. But numerous proteins from its genome are considered hypothetical proteins. Therefore, the present study aimed to reveal the functions of a hypothetical protein from the genome of S. coelicolor. Several bioinformatics tools were employed to predict the structure and function of this protein. Sequence similarity was searched through the available bioinformatics databases to find out the homologous protein. The secondary and tertiary structure were predicted and further validated with quality assessment tools. Furthermore, the active site and the interacting proteins were also explored with the utilization of CASTp and STRING server. The hypothetical protein showed the important biological activity having with two functional domain including POD-like_MBL-fold and rhodanese homology domain. The functional annotation exposed that the selected hypothetical protein could show the hydrolase activity. Furthermore, protein-protein interactions of selected hypothetical protein revealed several functional partners those have the significant role for the bacterial survival. At last, the current study depicts that the annotated hypothetical protein is linked with hydrolase activity which might be of great interest to the further research in bacterial genetics.

• MALSORI
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• v.55
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• pp.77-91
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• 2005

In this paper, we propose an XML based meta-data specification for industrial speech databases. Building speech databases is very time-consuming and expensive. Recently, by the government supports, huge amount of speech corpus has been collected as speech databases. However, the formats and meta-data for speech databases are different depending on the constructing institutions. In order to advance the reusability and portability of speech databases, a standard representation scheme should be adopted by all speech database construction institutions. ETRI proposed a XML based annotation scheme [51 for speech databases, but the scheme has too simple and flat modeling structure, and may cause duplicated information. In order to overcome such disadvantages in this previous scheme, we first define the speech database more formally and then identify object appearing in speech databases. We then design the data model for speech databases in an object-oriented way. Based on the designed data model, we develop the meta-data specification for industrial speech databases.

• Molecular & Cellular Toxicology
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• v.1 no.4
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• pp.281-283
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• 2005

Extraction of biologically meaningful data and their validation are very important for toxicogenomics study because it deals with huge amount of heterogeneous data. BINGO is an annotation mining tool for biological interpretation of gene groups. Several statistical modeling approaches using Gene Ontology (GO) have been employed in many programs for that purpose. The statistical methodologies are useful in investigating the most significant GO attributes in a gene group, but the coherence of the resultant GO attributes over the entire group is rarely assessed. BINGO complements the statistical methods with graph-theoretic measures using the GO directed acyclic graph (DAG) structure. In addition, BINGO visualizes the consistency of a gene group more intuitively with a group-based GO subgraph. The input group can be any interesting list of genes or gene products regardless of its generation process if the group is built under a functional congruency hypothesis such as gene clusters from DNA microarray analysis.

• Proceedings of the Korea Information Processing Society Conference
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• 2002.04a
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• pp.787-790
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• 2002

의미 기반 영상 검색은 Color, Texture, Region 정보, Spatial Color Distribution등의 저차원 특징 정보와 이미지 데이터에 의미를 부여하기 위해 주서 처리하는 것이 일반적이다. 그리고 부여된 키워드나 시소러스와 같은 어휘 사전을 이용하여 의미기반 정보검색을 수행하고 있지만, 기존의 키워드기반 텍스트 정보검색의 한계를 벗어나지 못하는 문제를 야기 시킨다. 이에 본 논문에서는 시각 데이터에 존재하는 객체들과 그 객체 사이의 개념관계를 Ontology의 한 형태인 WordNet을 이용하여 의미 정보로 표현할 수 있도록 한다. 이를 활용하면 영상 데이터의 자동 주석 시스템이나 검색 시스템에서 인간이 인식하는 개념적인 사고방식에 더욱 접근할 수 있는 결과물을 얻을 수 있을 것이다.

• Journal of the Korea Society of Computer and Information
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• v.16 no.7
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• pp.67-76
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• 2011

Recently, researches for semantic annotation methods which represent and search objects included in video data, have been briskly activated since video starts to be popularized as types for interactive contents. Different location data occurs at each frame because coordinates of moving objects are changed with the course of time. Saving the location data for objects of every frame is too ineffective. Thus, it is needed to compress and represent effectively. This paper suggests two methods; the first, ontology modeling for moving objects to make users intuitively understandable for the information, the second, to reduce the amount of data for annotating moving objects by using cubic spline interpolation. To verify efficiency of the suggested method, we implemented the interactive video system and then compared with each video dataset based on sampling intervals. The result follows : when we got samples of coordinate less than every 15 frame, it showed that could save up to 80% amount of data storage; moreover, maximum of error deviation was under 31 pixels and the average was less than 4 pixels.