• Journal of KIISE
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• v.42 no.12
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• pp.1584-1589
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• 2015

With the advancement of next-generation sequencing (NGS) technologies, various genome browsers have been introduced. Because existing browsers focus on comparison of the genomic data of extant species, however, there is a need for a genome browser for ancestral genomes and their evolution. In this paper, we introduce a genome browser, AGB (Ancestral Genome Browser), that displays ancestral genome data reconstructed from existing species. With AGB, it is possible to trace genomic variations that occurred during evolution in a simple and intuitive way. We explain the capability of AGB in terms of visualizing ancestral genomic information and evolutionary genomic variations. AGB is now available at http://bioinfo.konkuk.ac.kr/genomebrowser/.

• BMB Reports
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• v.45 no.1
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• pp.47-50
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• 2012

The International HapMap Project and the Human Genome Diversity Project (HGDP) provide plentiful resources on human genome information to the public. However, this kind of information is limited because of the small sample size in both databases. A Genome-Wide Association Study has been conducted with 8,842 Korean subjects as a part of the Korea Association Resource (KARE) project. In an effort to build a publicly available browsing system for genome data resulted from large scale KARE GWAS, we developed the KARE browser. This browser provides users with a large amount of single nucleotide polymorphisms (SNPs) information comprising 1.5 million SNPs from population-based cohorts of 8,842 samples. KAREBrowser was based on the generic genome browser (GBrowse), a web-based application tool developed for users to navigate and visualize the genomic features and annotations in an interactive manner. All SNP information and related functions are available at the web site http://ksnp.cdc. go.kr/karebrowser/.

• Genomics & Informatics
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• v.2 no.3
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• pp.147-148
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• 2004

Recently completed mitochondrial genome databses from public resources provide us with a better understanding of individual mitochondrial genomes for population genomics. By determining the substitution rate of the genomic sequences, it is plausible to derive dates on the phylogenetic tree and build a chronology of events in the evolution of human species. MitGEN is specially designed as a mitochondrial genome browser for analyzing, comparing and visualizing single nucleotide polymorphism for human mitochondrial genomes between human races for comparative genomics. It is a standalone application and is available free for non-commercial work.

• Journal of Plant Biotechnology
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• v.5 no.4
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• pp.197-200
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• 2003

Scalable Vector Graphics (SVG) has enabled a visually appealing, browser-based application for the display of Brassica sequences relative to Arabidopsis thaliana, and there are currently more than 70,000 B. napus Expressed Sequence Tags (ESTs) displayed. The client side of this browser is based on a Custom Graphical User Interface (CGUI) library which uses SVG, a new web graphics standard, to provide windowing functionality inside the web browser. This windowing functionality, combined with asynchronous data retrieval and client side rendering overcomes two of the key technology imposed drawbacks of current web based browsers: Fixed displays and frequent page reloads. The end result is an intuitive and enjoyable browsing experience. The browser is accessible online from the Brassica / Arabidopsis Genomics Initiative (http://brassica.agr.gc.ca). Inquiries about the browser should be directed to LewisCT@agr.gc.ca.

• Genomics & Informatics
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• v.15 no.4
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• pp.178-182
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• 2017

Next-generation sequencing (NGS) technology has become a trend in the genomics research area. There are many software programs and automated pipelines to analyze NGS data, which can ease the pain for traditional scientists who are not familiar with computer programming. However, downstream analyses, such as finding differentially expressed genes or visualizing linkage disequilibrium maps and genome-wide association study (GWAS) data, still remain a challenge. Here, we introduce a dockerized web application written in R using the Shiny platform to visualize pre-analyzed RNA sequencing and GWAS data. In addition, we have integrated a genome browser based on the JBrowse platform and an automated intermediate parsing process required for custom track construction, so that users can easily build and navigate their personal genome tracks with in-house datasets. This application will help scientists perform series of downstream analyses and obtain a more integrative understanding about various types of genomic data by interactively visualizing them with customizable options.

• Genomics & Informatics
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• v.6 no.2
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• pp.57-63
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• 2008

The Korean HapMap Project has been carried out for the last 5 years since it started in June, 2003. The project generated data for a sum of 1,764,000 Korean SNPs and formally registered the data to the dbSNP of NCBI (The dbSNP website. 2008). We have developed a series of software programs for association studies as well as for the comparison and analysis of Korean HapMap data with four other populations (CEPH, Yoruba, Han Chinese, and Japanese populations). The KHapmap Browser was developed and integrated to provide haplotype retrieval and comparative study tools of human ethnicities for comprehensive disease association studies (http://www.khapmap.org). On that basis, GBrowse was adopted in the KHapmap Browser for inherent Korean genetic data, and a provision of extended services was pledged with the distributed sequence annotation system (DAS). The dynamic linking service of the KHapmap Browser to other tools in our intranetwork environment provides many enhanced functions over GBrowse without DAS. KHapmap Browser is expected to be an invaluable tool for the study of Korean and international Hapmap data.

• Genomics & Informatics
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• v.10 no.1
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• pp.65-67
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• 2012

We have discovered copy number variations (CNVs) in 3,578 Korean individuals with the Affymetrix Genome-Wide SNP array 5.0, and 4,003 copy number variation regions (CNVRs) were defined in a previous study. To explore the details of the variants easily in related studies, we built a database, cataloging the CNVs and related information. This system helps researchers browsing these variants with gene and structure variant annotations. Users can easily find specific regions with search options and verify them from system-integrated genome browsers with annotations.

• Genomics & Informatics
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• v.3 no.3
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• pp.68-73
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• 2005

Pharmacogenomics research requires an intelligent integration of large-scale genomic and clinical data with public and private knowledge resources. We developed a web-based knowledge base for KPRN (Korea Pharmacogenomics Research Network, http://kprn.snubi. org/). Four major types of information is integrated; genetic variation, drug information, disease information, and literature annotation. Eighteen Korean pharmacogenomics research groups in collaboration have submitted 859 genotype data sets for 91 disease-related genes. Integrative analysis and visualization of the large collection of data supported by integrated biomedical path­ways and ontology resources are provided with a user-friendly interface and visualization engine empowered by Generic Genome Browser.

• BMB Reports
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• v.41 no.11
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• pp.757-764
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• 2008

The genomic sequences of a huge number of species have been determined. Typically, these genome sequences and the associated annotation data are accessed through Internet-based genome browsers that offer a user-friendly interface. Intelligent use of the data should expedite biological knowledge discovery. Such activity is collectively called data mining and involves queries that can be simple, complex, and even combinational. Various tools have been developed to make genome data mining available to computational and experimental biologists alike. In this mini-review, some tools that have proven successful will be introduced along with examples taken from published reports.

• Genomics & Informatics
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• v.2 no.2
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• pp.61-66
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• 2004

Fusion proteins resulting from chimeric sequences are excellent targets for therapeutic drug development. We developed a database of chimeric sequences by examining the genomic alignment of mRNA and EST sequences in the GenBank. We identified 688 chimeric mRNA and 20,998 chimeric EST sequences. Including EST sequences greatly expands the scope of chimeric sequences even though it inevitably accompanies many artifacts. Chimeric sequences are clustered according to the ECgene ID so that the user can easily find chimeric sequences related to a specific gene. Alignments of chimeric sequences are displayed as custom tracks in the UCSC genome browser. ChimerDB, available at http://genome.ewha.ac.kr/ECgene/ChimerDB/, should be a valuable resource for finding drug targets to treat cancers.