• 한국육종학회지
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• 제40권1호
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• pp.1-7
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• 2008

An attempt was made to link rice embryo proteins to DNA sequences and to understand their functions. One hundred of the 700 spots detected on the embryo 2-DE gels were microsequenced. Of these, 28% of the embryo proteins were matched to DNA sequences with known functions, but 72% of the proteins were unknown in functions as previously reported (Woo et al. 2002). In addition, twenty-four protein spots with 100% of homology and nine with over 80% were matched to ESTs (expressed sequence tags) after expanding the amino acid sequences of the protein spots by Database searches using the available rice EST databases at the NCBI (http://www/ncbi.nlm.nih.gov/) and DDBJ (http://www.ddbj.nig.ac.jp/). The chromosomal location of some proteins were also obtained from the rice genetic map provided by Japanese Rice Genome Research Program (http://rgp.dna.affrc.go.jp). The DNA sequence databases including EST have been reported for rice (Oryza sativa L.) now provides whole or partial gene sequence, and recent advances in protein characterization allow the linking proteins to DNA sequences in the functional analysis. This work shows that proteome analysis could be a useful tool strategy to link sequence information and to functional genomics.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.407-411
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• 2005

KUGI (Korean UniGene Information) database contains the annotation information of the cDNA sequences obtained from the disease samples prevalent in Korean. A total of about 157,000 5'-EST high throughput sequences collected from cDNA libraries of stomach, liver, and some cancer tissues or established cell lines from Korean patients were clustered to about 35,000 contigs. From each cluster a representative clone having the longest high quality sequence or the start codon was selected. We stored the sequences of the representative clones and the clustered contigs in the KUGI database together with their information analyzed by running Blast against RefSeq, human mRNA, and UniGene databases from NCBI. We provide a web-based search engine fur the KUGI database using two types of user interfaces: attribute-based search and similarity search of the sequences. For attribute-based search, we use DBMS technology while we use BLAST that supports various similarity search options. The search system allows not only multiple queries, but also various query types. The results are as follows: 1) information of clones and libraries, 2) accession keys, location on genome, gene ontology, and pathways to public databases, 3) links to external programs, and 4) sequence information of contig and 5'-end of clones. We believe that the KUGI database and search system may provide very useful information that can be used in the study for elucidating the causes of the disease that are prevalent in Korean.

• Asian-Australasian Journal of Animal Sciences
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• 제23권11호
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• pp.1399-1404
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• 2010

We have created a Bovine Genome Database, an integrated genomic resource for Bos taurus, by merging bovine data from various databases and our own data. We produced 55,213 Korean cattle (Hanwoo) ESTs from cDNA libraries from three tissues. We concentrated on genomic information based on Hanwoo transcripts and provided user-friendly search interfaces within the Bovine Genome Database. The genome browser supported alignment results for the various types of data: Hanwoo EST, consensus sequence, human gene, and predicted bovine genes. The database also provides transcript data information, gene annotation, genomic location, sequence and tissue distribution. Users can also explore bovine disease genes based on comparative mapping of homologous genes and can conduct searches centered on genes within user-selected quantitative trait loci (QTL) regions. The Bovine Genome Database can be accessed at http://bgd.nabc.go.kr.

• 한국패류학회지
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• 제31권3호
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• pp.243-247
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• 2015

A stand-alone BLAST server is available that provides a convenient and amenable platform for the analysis of molluscan sequence information especially the EST sequences generated by traditional sequencing methods. However, it is found that the server has limitations in the annotation of molluscan sequences generated using next-generation sequencing (NGS) platforms due to inconsistencies in molluscan sequence available at NCBI. We constructed a web-based interface for a new stand-alone BLAST, called PANM-DB (Protostome DB) for the analysis of molluscan NGS data. The PANM-DB includes the amino acid sequences from the protostome groups-Arthropoda, Nematoda, and Mollusca downloaded from GenBank with the NCBI taxonomy Browser. The sequences were translated into multi-FASTA format and stored in the database by using the formatdb program at NCBI. PANM-DB contains 6% of NCBInr database sequences (as of 24-06-2015), and for an input of 10,000 RNA-seq sequences the processing speed was 15 times faster by using PANM-DB when compared with NCBInr DB. It was also noted that PANM-DB show two times more significant hits with diverse annotation profiles as compared with Mollusks DB. Hence, the construction of PANM-DB is a significant step in the annotation of molluscan sequence information obtained from NGS platforms. The PANM-DB is freely downloadable from the web-based interface (Malacological Society of Korea, http://malacol.or/kr/blast) as compressed file system and can run on any compatible operating system.

• ETRI Journal
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• 제29권2호
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• pp.249-251
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• 2007

A novel idea is presented to locate intersections in a video sequence captured from a moving vehicle. More specifically, we propose a Bayesian network approach to combine evidence extracted from a video sequence and evidence from a database, maximizing evidence from various sensors in a systematic manner and locating intersections robustly.

• 산업공학
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• 제14권2호
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• pp.158-163
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• 2001

The paper describes disassemblability evaluation method using axiomatic approach. In recent industry, it is necessary to develope high recyclable environmental product due to green consumer and environmental regulations. Disassembly stage is prior to recycling. Disaassembly time data is determined previously in order to calculate the disassembly segments and disassembly sequence. In this paper the evaluation method of disassembly segment/sequence and disassembly time database are suggested. A case study of monitor product was showed.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 1999년도 가을 학술발표논문집 Vol.26 No.2 (1)
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• pp.340-342
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• 1999

시퀀스 데이터(sequence data)에서는 각 데이터 값보다는 전후 그들 사이의 변화추세 등이 더 큰 정보로 작용하는 것이 일반적이다. 본문에서는 시퀀스 데이터베이스를 대상으로 하여 주어진 시퀀스 패턴과 모양이 유사한 모든 부분시퀀스를 검색해 내는 새로운 방식을 제안한다. 본 방식에서는 시퀀스 데이터의 모양 추출을 위한 데이터 변환, 유사 모양 패턴 클러스터링, 새로운 유사도 계산 방식 등을 도입함으로써, 기존의 방식이 매우 제한적인 패턴만을 유사패턴으로 간주하던 것에 비하여, 패턴이 데이터축 혹은 타임축으로 각각 확대, 축소, 이동된 경우에도 유사패턴으로 검색이 가능하다.

• 한국산업정보학회논문지
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• 제17권3호
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• pp.43-49
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• 2012

현재 운용되고 있는 리가시 시스템에 대한 요구명세서는 대부분 자료흐름도를 사용하고 있어, 시스템의 유지 보수를 위해서는 자료흐름도로부터 획득한 정보에 의존하지 않을 수 없다. 본 논문에서는 자료흐름도로부터 데이터베이스 테이블 설계순서를 추출하는 추출기를 설계, 구현하였다. 추출기는 자료흐름도를 입력 받아 저장하고, 이를 방향그래프로 변환하여 데이터베이스 테이블 설계순서를 추출하여 제시한다. 구현된 추출기는 실제 운용 중인 소프트웨어 시스템에 적용함으로써 실제 적용가능성을 보였다.

• 산업기술연구
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• 제21권A호
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• pp.147-153
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• 2001

This paper presents techniques for discovering rules with elastic patterns. Elastic patterns are useful for discovering rules from data sequences with different sampling rates. For fast discovery of rules whose heads and bodies are elastic patterns, we construct a suffix tree from succinct forms of data sequences. The suffix tree is a compact representation of rules, and is also used as an index structure for finding rules matched to a target head sequence. When matched rules cannot be found, the concept of rule relaxation is introduced. Using a cluster hierarchy and a relaxation error, we find the least relaxed rules that provide the most specific information on a target head sequence. Performance evaluation through extensive experiments reseals the effectiveness of the proposed approach.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.28-31
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• 2000

We describe a hidden Markov model, HMMTIR, for general protein sequence based on the I-sites library of sequence-structure motifs. Unlike the linear HMMs used to model individual protein families, HMMSTR has a highly branched topology and captures recurrent local features of protein sequences and structures that transcend protein family boundaries. The model extends the I-sites library by describing the adjacencies of different sequence-structure motifs as observed in the database, and achieves a great reduction in parameters by representing overlapping motifs in a much more compact form. The HMM attributes a considerably higher probability to coding sequence than does an equivalent dipeptide model, predicts secondary structure with an accuracy of 74.6% and backbone torsion angles better than any previously reported method, and predicts the structural context of beta strands and turns with an accuracy that should be useful for tertiary structure prediction. HMMSTR has been incorporated into a public, fully-automated protein structure prediction server.