• Journal of Microbiology and Biotechnology
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• v.22 no.9
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• pp.1208-1213
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• 2012

Microcystis aeruginosa is a cyanobacterium that can form harmful algal blooms (HABs) producing toxic secondary metabolites. We provide here draft genome information of four strains of this freshwater cyanobacterium that was obtained by the Next Generation Sequencing approach to provide a better understanding of molecular mechanisms at the physiological and ecological levels. After gene assembly, genes of each strain were identified and annotated, and a genome database and G-browser of M. aeruginosa were subsequently constructed. Such genome information resources will enable us to obtain useful information for molecular ecological studies with a better understanding of modulating mechanisms of environmental factors associated with blooming.

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.04a
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• pp.200-200
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• 2005

• Proceedings of the Korean Information Science Society Conference
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• 2008.06c
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• pp.198-202
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• 2008

많은 양의 유전자 정보가 유전공학의 발전과 Genome 프로젝트의 결과로 축적되고 있으며, 이러한 유전자 정보를 체계적으로 관리하고 가시화하기 위한 생물정보학 분야의 연구가 진행되고 있다. 기존의 많은 Genome Browser들이 완성된 형태의 툴로 서비스되고 있다. 이러한 툴들은 다목적의 많은 기능을 포함하고 있어 특정연구를 진행해야하는 연구자들은 너무 많은 정보로부터 원하는 것을 찾기 위해 시간과 노력이 필요하게 된다. 본 논문에서는 특정한 목적의 Gene 가시화 툴을 제작할 수 있는 Component Ware를 제안하고 이를 이용한 진화분석용 가시화 툴을 소개한다.

• Genomics & Informatics
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• v.6 no.2
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• pp.91-94
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• 2008

Single nucleotide polymorphisms (SNPs) are the most abundant form of human genetic variation and are a resource for mapping complex genetic traits. A genome is covered by millions of these markers, and researchers are able to compare which SNPs predominate in people who have a certain disease. The International HapMap Project, launched in October, 2002, motivated us to start the Korean HapMap Project in order to support Korean HapMap infrastructure development and to accelerate the finding of genes that affect health, disease, and individual responses to medications and environmental factors. A Korean SNP and haplotype database system was developed through the Korean HapMap Project to provide Korean researchers with useful data-mining information about disease-associated biomarkers for studies on complex diseases, such as diabetes, cancer, and stroke. Also, we have developed a series of software programs for association studies as well as the comparison and analysis of Korean HapMap data with other populations, such as European, Chinese, Japanese, and African populations. The developed software includes HapMapSNPAnalyzer, SNPflank, HWE Test, FESD, D2GSNP, SNP@Domain, KMSD, KFOD, KFRG, and SNP@WEB. We developed a disease-related SNP retrieval system, in which OMIM, GeneCards, and MeSH information were integrated and analyzed for medical research scientists. The kHapMap Browser system that we developed and integrated provides haplotype retrieval and comparative study tools of human ethnicities for comprehensive disease association studies (http://www.khapmap.org). It is expected that researchers may be able to retrieve useful information from the kHapMap Browser to find useful biomarkers and genes in complex disease association studies and use these biomarkers and genes to study and develop new drugs for personalized medicine.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.11
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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.

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.337-337
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• 2005

• Genomics & Informatics
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• v.3 no.3
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• pp.53-62
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• 2005

MicroRNAs play an important role in regulating gene expression, but their target identification is a difficult task due to their short length and imperfect complementarity. Burge and coworkers developed a program called TargetScan that allowed imperfect complementarity and established a procedure favoring targets with multiple binding sites conserved in multiple organisms. We improved their algorithm in two major aspects - (i) using well-defined UTR (untranslated region) database, (ii) examining the extent of conservation inside the 3' UTR specifically. Average length in our UTR database, based on the ECgene annotation, is more than twice longer than the Ensembl. Then, TargetScan was used to identify putative binding sites. The extent of conservation varies significantly inside the 3' UTR. We used the 'tight' tracks in the UCSC genome browser to select the conserved binding sites in multiple species. By combining the longer 3' UTR data, TargetScan, and tightly conserved blocks of genomic DNA, we identified 107 putative target genes with multiple binding sites conserved in multiple species, of which 85 putative targets are novel.

• Genomics & Informatics
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• v.16 no.3
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• pp.65-70
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• 2018

The non-coding DNA in eukaryotic genomes encodes a language which programs chromatin accessibility, transcription factor binding, and various other activities. The objective of this short report was to determine the impact of primary DNA sequence on the epigenomic landscape across 200-base pair genomic units by integrating nine publicly available ChromHMM Browser Extensible Data files of the Encyclopedia of DNA Elements (ENCODE) project. The nucleotide frequency profiles of nine chromatin annotations with the units of 200 bp were analyzed and integrative Markov chains were built to detect the Markov properties of the DNA sequences in some of the active chromatin states of different ChromHMM regions. Our aim was to identify the possible relationship between DNA sequences and the newly built chromatin states based on the integrated ChromHMM datasets of different cells and tissue types.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.6
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• pp.2489-2493
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• 2015

Background: Loss of heterozygosity (LOH) on chromosomal regions is crucial in tumor progression and this study aimed to identify genome-wide LOH in pancreatic cancer. Materials and Methods: Single-nucleotide polymorphism (SNP) profiling data GSE32682 of human pancreatic samples snap-frozen during surgery were downloaded from Gene Expression Omnibus database. Genotype console software was used to perform data processing. Candidate genes with LOH were screened based on the genotype calls, SNP loci of LOH and dbSNP database. Gene annotation was performed to identify the functions of candidate genes using NCBI (the National Center for Biotechnology Information) database, followed by Gene Ontology, INTERPRO, PFAM and SMART annotation and UCSC Genome Browser track to the unannotated genes using DAVID (the Database for Annotation, Visualization and Integration Discovery). Results: The candidate genes with LOH identified in this study were MCU, MICU1 and OIT3 on chromosome 10. MCU was found to encode a calcium transporter and MICU1 could encode an essential regulator of mitochondrial $Ca^{2+}$ uptake. OIT3 possibly correlated with calcium binding revealed by the annotation analyses and was regulated by a large number of transcription factors including STAT, SOX9, CREB, NF-kB, PPARG and p53. Conclusions: Global genomic analysis of SNPs identified MICU1, MCU and OIT3 with LOH on chromosome 10, implying involvement of these genes in progression of pancreatic cancer.

• Journal of Plant Biotechnology
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• v.47 no.3
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• pp.218-226
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• 2020

This report describes methods for selecting informative single nucleotide polymorphisms (SNPs), and the development of an online Solanaceae genome database, using 234 tomato resequencing data entries deposited in the NCBI SRA database. The 126 accessions of Solanum lycopersicum, 68 accessions of Solanum lycopersicum var. cerasiforme, and 33 accessions of Solanum pimpinellifolium, which are frequently used for breeding, and some wild-species tomato accessions were included in the analysis. To select tag-SNPs, we identified 29,504,960 SNPs in 234 tomatoes and then separated the SNPs in the genic and intergenic regions according to gene annotation. All tag-SNP were selected from non-synonymous SNPs among the SNPs present in the gene region and, as a result, we obtained tag-SNP from 13,845 genes. When there were no non-synonymous SNPs in the gene, the genes were selected from synonymous SNPs. The total number of tag-SNPs selected was 27,539. To increase the usefulness of the information, a Solanaceae genome database website, TGsol (http://tgsol. seeders.co.kr/), was constructed to allow users to search for detailed information on resources, SNPs, haplotype, and tag-SNPs. The user can search the tag-SNP and flanking sequences for each gene by searching for a gene name or gene position through the genome browser. This website can be used to efficiently search for genes related to traits or to develop molecular markers.