• Journal of the Korea Organic Resources Recycling Association
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• v.17 no.4
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• pp.48-58
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• 2009

Glycosyl hydrolases (GH, EC 3.2.1.-) are key enzymes which can hydrolyze the glycosidic bonds between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. The new enzyme nomenclature of glycoside hydrolases is based on their amino acid sequence similarity and structural features. Here, we examined the glycosyl hydrolase family(GHF) genes reported from earthworm species. Among overall 115 GHFs, 12 GHFs could be identified from earthworm species through CAZy database. Of 12 GHF group genes, five genes including GHF2, 5, 17, 18, 20 are thought to be potent for industrial applications. The alignment of these genes with same genes from other animal species exhibited high sequence homology and some important amino acid residues necessary for enzyme activity appeared to be conserved. These genes can be utilized as a pest control agent or applicable to the food industry, clinical therapeutics and organic wastes disposition.

• The KIPS Transactions:PartB
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• v.11B no.5
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• pp.611-618
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• 2004

This paper addresses the design and implementation of class distribution in distributed object-oriented databases. The proposed strategy of distribution consists of two-step design of fragments. One is class fragmentation and the other is allocation of fragments. In step of class fragmentation, we have defined partitioning algorithms to reflect the characteristics of object-oriented databases such as method, inheritance and composite-object. In step of allocation, we have defined the objective function for allocation considering system operating cost including storage, query processing and communication and implemented it using Genetic Algorithm.

• Horticultural Science & Technology
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• v.29 no.2
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• pp.116-122
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• 2011

In this study, we report the generation and analysis of 1,392 expressed sequence tags (ESTs) from Korean Stewartia (Stewartia koreana Nakai). A cDNA library was generated from the young leaf tissue and a total of 1,392 cDNA were partially sequenced. EST and unigene sequence quality were determined by computational filtering, manual review, and BLAST analyses. Finally, 1,301 ESTs were acquired after the removal of the vector sequence and filtering over a minimum length 100 nucleotides. A total of 893 unigene, consisting of 150 contigs and 743 singletons, was identified after assembling. Also, we identified 95 new microsatellite-containing sequences from the unigenes and classified the structure according to their repeat unit. According to homology search with BLASTX against the NCBI database, 65% of ESTs were homologous with known function and 11.6% of ESTs were matched with putative or unknown function. The remaining 23.2% of ESTs showed no significant similarity to any protein sequences found in the public database. Annotation based searches against multiple databases including wine grape and populus sequences helped to identify putative functions of ESTs and unigenes. Gene ontology (GO) classification showed that the most abundant GO terms were transport, nucleotide binding, plastid, in terms biological process, molecular function and cellular component, respectively. The sequence data will be used to characterize potential roles of new genes in Stewartia and provided for the useful tools as a genetic resource.

• Journal of Information Management
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• v.40 no.4
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• pp.109-133
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• 2009

Among biological information, GenBank, provided by the National Center for Biotechnology Information (NCBI)of the United States, is a representative database on genetic information and is the most widely used by researchers around the world. Korea Institute of Science and Technology Information (KISTI) visits NCBI on a regular basis and downloads the latest version of GenBank to reorganize the information gathered there into a database. This database is provided for Korean researchers of science and technology through the Bio-KRISTAL search engine, developed by KISTI. This study aims to design a service model that links information on papers, patents, and biodiversity and other contents of NDSL, an integrated service on scientific and technological information run by KISTI, with GenBank's reference and organism fields and to develop a prototype system. For this purpose, this paper explores the possibility of a linkage and convergence service between heterogeneous content by: (a) collecting GenBank data from NCBI's FTP site; (b) dividing GenBank text files into basic and reference genetic information and restructuring them into a database; (c) extracting article and patent information from the GenBank reference fields to generate new tables; and (d) leveraging data mapping technology to implement a prototype system where GenBank and NDSL data are interlinked and provided.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.55 no.2
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• pp.151-158
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• 2010

Camelina sativa L., known as popular names "gold-of-pleasure" or "false flax" is an alternative oilseed crop that can be grown under different climatic and soil conditions. Up to date, however, the genomic information of Camelina has not been studied in detail. Therefore, a cDNA library was constructed and characterized from young leaves. The constructed cDNA library incorporated of 1334 cDNA clones and the size of the insertion fragments average was 736 base pair. We generated a total of 1269 high-quality expressed sequence tags (ESTs) sequences. The result of cluster analysis of EST sequences showed that the number of unigene was 851. According to subsequent analysis, the 476 (55.9%) unigenes were highly homologous to known function genes and the other 375 (44.1%) unigenes were unknown. Remaining 63 (7.4%) unigenes had no homology with any other peptide in NCBI database, indicating that these seemed to be novel genes expressed in leaves of Camelina. The database-matched ESTs were further classified into 17 categories according to their functional annotation. The most abundant of categories were "protein with binding function or cofactor requirement (27%)", "metabolism (11%)", "subcellular localization (11%)", "cellular transport, transport facilities and transport routes (7%)", "energy (6%)", "regulation of metabolism and protein function (6%)". Our result in this study provides an overview of mRNA expression profile and a basal genetic information of Camelina as an oilseed crop.

• Korean Journal of Ecology and Environment
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• v.55 no.4
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• pp.352-359
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• 2022

Recently, with the development of genetic technology, interest in environmental DNA (eDNA) to study biodiversity according to molecular biological approaches is increasing. Environmental DNA has many advantages over traditional research methods for biological communities distributed in the environment but highly depends on the established base sequence database. This study conducted a comprehensive analysis of the habitat status and classification at the genus level, which is mainly used in eDNA (12S rRNA, 16S rRNA, 18S rRNA, COI, and CYTB), focusing on Korean registration taxon groups (phytoplankton, zooplankton, macroinvertebrates, and fish). As a result, phytoplankton and zooplankton showed the highest taxa proportion in 18S rRNA, and macroinvertebrates observed the highest ratio in the nucleotide sequence database in COI. In fish, all genes except 18S rRNA showed a high taxon ratio. Based on the Korean registration taxon group, the gene construction of the top 20 genera according to bio density observed that most of the phytoplankton were registered in 18S rRNA, and the most significant number of COI nucleotide sequences were established in macroinvertebrates. In addition, it was confirmed that there is a nucleotide sequence for the top 20 genera in 12S rRNA, 16S rRNA, and CYTB in fish. These results provided comprehensive information on the genes suitable for eDNA research for each taxon group.

• Journal of Sericultural and Entomological Science
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• v.38 no.1
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• pp.13-18
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• 1996

To secure the genetic resources of silkworm, Bomyx mori, the cDNA library was constructed with mRNA isolated from fifth instar larvae. Titer of the cDNA library was about 1.3 X 106 plaques in total. We presumed that the titer covered all transcripts existed in Bombyx mori. Meanwhile, it is knowen that partial cDNA sequences, Expressed Sequence Tags(ESTs), have a good value for the discovery of novel genes and the elucidation of their structures. For this purpose, partial cDNA sequencing was carried out from randomly selected cDNA clones in the library. Partial cDNA sequences of 37 clones were determined and an average of 212 nucleotides of sequence can be read from the clone. The ESTs were searched in GenBAnk database and fifteen ESTs showed significant similarities to enlisted sequences. They included the genes of storage protein, heat shock protein, actin, catalase and so forth. We presumed that the 22 unmatched ESTs were novel genes.

• Proceedings of the Korea Multimedia Society Conference
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• 2002.11b
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• pp.792-795
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• 2002

현재 많은 관심의 대상이 되고 있는 데이터 마이닝은 대용량의 데이터베이스로부터 일정한 패턴을 분류하여 지식의 형태로 추출하는 작업이다. 데이터 마이닝의 대표적인 기법인 군집화는 군집내의 유사성을 최대화하고 군집들간의 유사성을 최소화 시키도록 데이터 집합을 분할하는 것이다. 데이터 마이닝에서 군집화는 대용량 데이터를 다루기 때문에 원시 데이터에 대한 접근 횟수를 줄이고 알고리즘이 다루어야 할 데이터 구조의 크기를 줄이는 군집화 기법이 활발하게 사용된다. 그런데 기존의 군집화 알고리즘은 잡음에 매우 민감하고, local minima에 반응한다. 또한 사전에 군집의 개수를 미리 결정해야 하고, initialization 값에 따라 군집의 성능이 좌우되는 문제점이 있다. 본 연구에서는 유전자 알고리즘을 이용하여 자동으로 군집의 개수를 결정하는 LONGEPRO 알고리즘을 제안하고, 여기서 제시하는 적합도 함수의 최적화된 군집을 찾아내여 조금더 효율적인 알고리즘을 만들어 대용량 데이터를 다루는 데이터 마이닝에 적용해 보려 한다.

• Journal of KIISE:Software and Applications
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• v.26 no.3
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• pp.422-430
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• 1999

멀티미디어 영상검색 중 영상의 내용을 기반으로 한 검색방법에 관한 연구가 활발히 진행되고 있다. 이는 기존의 키워드기반 영상검색 방법에 비해 효율적인 관리와 검색 방법을 제공하고 있다. 그러나 대부분의 방법이 단순한 공학적 방법에 치우쳐 사람의 감성과는 무관한 검색 결과를 제공한다. 이러한 문제점을 해결하기 위해 본 논문에서는 대화형 유전자 알고리즘을 도입하여 검색과정에 사람의 감성을 반영할 수 있는 방법을 제안한다. 이 방법은 구체적으로 표현될 수 있는 영상 뿐 아니라 우울한 느낌의 영상, 즐거운 느낌의 영상과 같은 추상적인 느낌의 영상을 검색할수 있도록 한다. 2000개의 영상으로 이루어진 데이터베이스로 실험한 결과 , 제안한 방법이 유용함을 알 수 있었다.

• Proceedings of the Korea Contents Association Conference
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• 2009.05a
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• pp.870-874
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• 2009

Genetic algorithms can be effectively used when generating abstract images in an automatic way. However, managing huge number of automatically generated images has been problematic without sufficient managing mechanisms. This paper presents effective classification scheme for the abstract Affine images using form, emotion and color facets, and implements image databases.