• Journal of KIISE:Databases
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• v.30 no.2
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• pp.209-224
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• 2003

Recent development of electronic commerce enables the use of Electronic Stock Trading Systems(ESTS) to be expanded. In ESTS, information with various sensitivity levels is shared by multiple users with mutually different clearance levels. Therefore, it is necessary to use Multilevel Secure Database Management Systems(MLS/DBMSs) in controlling concurrent execution among multiple transactions. In ESTS, not only analytical OLAP transactions, but also mission critical OLTP transactions are executed concurrently, which causes it difficult to adapt traditional secure transaction management schemes to ESTS environments. In this paper, we propose Secure One Snapshot(SOS) protocol that is devised for Secure Transaction Management in ESTS. By maintaining additional one snapshot as well as working database SOS blocks covert-channel efficiently, enables various real-time transaction management schemes to be adapted with ease, and reduces the length of waiting queue being managed to maintain freshness of data by utilizing the characteristics of less strict correctness criteria. In this paper, we introduce the process of SOS protocol with some examples, and then analyze correctness of devised protocol.

• Genomics & Informatics
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• v.3 no.3
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• pp.86-93
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• 2005

Human brain EST data provide important clues for our understanding of the molecular biology associated with the function of the normal brain and the molecular pathophysiology with brain disorders. To systematically and efficiently study the function and disorders of the human brain, 45,773 human brain ESTs were collected from 27 human brain cDNA libraries, which were constructed from normal brains and brain disorders such as brain tumors, Parkinson's disease (PO) and epilepsy. An analysis of 45,773 human brain ESTs using our EST analysis pipeline resulted in 38,396 high-quality ESTs and 35,906 ESTs, which were coalesced into 8,246 unique gene clusters, showing a significant similarity to known genes in the human RefSeq, human mRNAs and UniGene database. In addition, among 8,246 gene clusters, 4,287 genes ($52\%$) were found to contain full-length cONA clones. To facilitate the extraction of useful information in collected these human brain ESTs, we developed a user-friendly interface system, the Korea Brain Unigene Database (KBUD). The KBUD web interface allows access to our human brain data through three major search modes, the BioCarta pathway, keywords and BLAST searches. Each result when viewed in KBUD offers comprehensive information concerning the analyzed human brain ESTs provided by our data as well as data linked to various other publiC databases. The user-friendly developed KBUD, the first world-wide web interface for human brain EST data with ESTs of human brain disorders as well as normal brains, will be a helpful system for developing a better understanding of the underlying mechanisms of the normal brain well as brain disorders. The KBUD system is freely accessible at http://kugi.kribb.re.kr/KU/cgi -bin/brain. pI.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.2
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• pp.170-178
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• 2005

An in silico approach was developed to survey the genes expressed in four internal organs of pig: liver, kidney, spleen and small intestine. The major procedures of the approach included: (1) BLAST searching against GenBank "est_others" database using human cDNA sequences as queries to screen the porcine orthologous expressed sequence tags (ESTs), (2) classifying the porcine ESTs records by resources according to certain criteria and (3) analyzing data for ESTs specifically expressed in each organ. In order to do so, four Java programs were developed. Based on the ESTs available in the GenBank database, it was found that there were at least 2,100 genes expressed in these four organs, including 128 in the liver, 81 in the kidney, 780 in the spleen, and 1,423 in the small intestine respectively (a few genes co-expressed in these tissues). Gene expression patterns, such as co-expressed genes, preferentially expressed genes and basic active genes were also compared and characterized among these organs. This study provides a comprehensive model on how to use the bioinformatics approach and Genbank databases to facilitate the discovery of new genes in livestock species.

• Korean Journal of Agricultural Science
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• v.38 no.1
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• pp.11-16
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• 2011

In this study, we report the generation and analysis of a total of 1,211 expressed sequence tags (ESTs) from Pinus koraiensis. A cDNA library was generated from the young leaf tissue and a total of 1,211 cDNA were partially sequenced. EST and unigene sequence quality were determined by computational filtering, manual review, and BLAST analyses. In all, 857 ESTs were acquired after the removal of the vector sequence and filtering over a minimum length 50 nucleotides. A total of 411 unigene, consisting of 89 contigs and 322 singletons, was identified after assembling. Also, we identified 77 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, 63.1% of ESTs were homologous with known function and 22.2% of ESTs were matched with putative or unknown function. The remaining 14.6% of ESTs showed no significant similarity to any protein sequences found in the public database. 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 Pinus and provided for the useful tools as a genetic resource.

• The Plant Pathology Journal
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• v.20 no.1
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• pp.46-51
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• 2004

Host resistance is usually parasite-specific and is restricted to a particular pathogen races, and commonly is expressed against specific pathogen genotypes. In contrast, resistance shown by an entire plant species to a species of pathogen is known as non-host resistance. Therefore, non-host resistance is the more common and broad form of disease resistance exhibited by plants. As a first step to understand the mechanism of non-host plant defense, expressed sequence tags (EST) were generated from a hot pepper leaf cDNA library constructed from combined leaves collected at different time points after inoculation with non-host soybean pustule pathogen (Xanthomonas axonopodis pv. Glycines; Xag). To increase gene diversity, ESTs were also generated from cDNA libraries constructed from anthers and flower buds. Among a total of 10,061 ESTs, 8,525 were of sufficient quality to analyze further. Clustering analysis revealed that 55 ％ of all ESTs (4685) occurred only once. BLASTX analysis revealed that 74％ of the ESTs had significant sequence similarity to known proteins present in the NCBI nr database. In addition, 1,265 ESTs were tentatively identified as being full-length cDNAs. Functional classification of the ESTs derived from pathogen-infected pepper leaves revealed that about 25％ were disease- or defense-related genes. Furthermore, 323 (7％) ESTs were tentatively identified as being unique to hot pepper. This study represents the first analysis of sequence data from the hot pepper plant species. Although we focused on genes related to the plant defense response, our data will be useful for future comparative studies.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.21-22
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• 2000

Expressed sequence tags (EFTs) are the partial segments of cDNA produced from 5 or 3 single-pass sequencing of cDNA clones, error-prone and generated in highly redundant sets. Advancement and expansion of Genomics made biologists to generate huge amount of ESTs from variety of organisms-human, microorganisms as well as plants, and the cumulated number of ESTs is over 5.3 million, As the EST data being accumulate more rapidly, it becomes bigger that the needs of the EST analysis tools for extraction of biological meaning from EST data. Among the several needs of EST analyses, the extraction of protein sequence or functional motifs from ESTs are important for the identification of their function in vivo. To accomplish that purpose the precise and accurate identification of the region where the coding sequences (CDSs) is a crucial problem to solve primarily, and it will be helpful to extract and detect of genuine CD5s and protein motifs from EST collections. Although several public tools are available for EST analysis, there is not any one to accomplish the object. Furthermore, they are not targeted to the plant ESTs but human or microorganism. Thus, to correspond the urgent needs of collaborators deals with plant ESTs and to establish the analysis system to be used as general-purpose public software we constructed the pipelined-EST analysis system by integration of public software components. The software we used are as follows - Phred/Cross-match for the quality control and vector screening, NCBI Blast for the similarity searching, ICATools for the EST clustering, Phrap for EST contig assembly, and BLOCKS/Prosite for protein motif searching. The sample data set used for the construction and verification of this system was 1,386 ESTs from human intrathymic T-cells that verified using UniGene and Nr database of NCBI. The approach for the extraction of CDSs from sample data set was carried out by comparison between sample data and protein sequences/motif database, determining matched protein sequences/motifs that agree with our defined parameters, and extracting the regions that shows similarities. In recent future, in addition to these components, it is supposed to be also integrated into our system and served that the software for the peptide mass spectrometry fingerprint analysis, one of the proteomics fields. This pipelined-EST analysis system will extend our knowledge on the plant ESTs and proteins by identification of unknown-genes.

• 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 Sericultural and Entomological Science
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• v.38 no.1
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• pp.19-24
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• 1996

To investigate the genes which is related to immune reaction of Bombyx mori, differential screening was carried out using naive and induced B. mori mRNA probe. To begin with, we constructed the cDNA library with mRNA isolated from fifth instar larvae injected with E. coli(4 X 106 cells/larva) using Uni ZAP XR vector kit. Thirty-two inducible cDNAs showing higher intensity on the induced mRNA probing membranes were selected. Partial nucleotide sequences of 29 clones were determined and their expessed sequence tags (ESTs) were produced. Nineteen ESTs in 29 ESTs were matched in GenBank database and the rest of them were found to be unknown. These unmatched ESTs were presumed to be novel genes. The nineteen ESTs contained variable genes related to biological process in Bombyx mori and four classes immune genes. Four clones, BmInc 6, 8, 18 and 27 were similar to two antibacterial peptide genes, hemolin gene and transferrin gene, respectively.

• Journal of Sericultural and Entomological Science
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• v.51 no.2
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• pp.191-196
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• 2013

This study was aimed for development of a useful genes that has a transcript expressional specificity in the early embryonic stage of the silkworm, Bombyx mori. We constructed and analyzed a full-length cDNA library from silkworm's eggs which after a lapse of 2 ~ 6 hours post oviposit. A total 960 clones were randomly selected, and the 5' ends of the inserts were sequenced to generate 652 expressed sequence tags(EST). 334 unique ESTs were generated after the assembly of 652 ESTs. The annotation of 334 unique ESTs by BLAST search revealed that 156(47%) of the sequences represented known genes, whereas 178(53%) of the sequences has no matches in the database. Of the 156 known genes, the most abundant genes were heat shock protein hsp20.8 gene(12 times) and ubiqutin-like protein gene(11 times). The functional groups of these ESTs with matches in the database were constructed according to their putative molecular functions. Among thirteen functional categories, the largest groups were protein synthesis(9.6%) and cellular organization( 8.1%). Further defined studies on molecular functions and biological roles of their promoters will give us wellfined information and its application.

• Parasites, Hosts and Diseases
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• v.43 no.4 s.136
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• pp.149-156
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• 2005

Four hundred and sixty five randomly selected clones from a cDNA library of Blattella germanica were partially sequenced and searched using BLAST as a means of analyzing the transcribed sequences of its genome. A total of 363 expressed sequence tags (ESTs) were generated from 465 clones after editing and trimming the vector and ambiguous sequences. About $42\%$ (154/363) of these clones showed significant homology with other data base registered genes. These new B. germanica genes constituted a broad range of transcripts distributed among ribosomal proteins, energy metabolism, allergens, proteases, protease inhibitors, enzymes, translation, cell signaling path-ways, and proteins of unknown function. Eighty clones were not well-matched by database searches, and these rep-resent new B. germanica-specific ESTs. Some genes which drew our attention are discussed. The information obtained increases our understanding of the B. germanica genome.