1.New Approach to the Analysis of Palindromic Structure in Genome Sequences.
Seok Won KIM ; Yong Seok LEE ; Sang Haeng CHOI ; Sung Hwa CHAE ; Dae Won KIM ; Hong Seog PARK
Genomics & Informatics 2006;4(4):167-169
PABAP (Palindrome Analysis by BLAST Program) is an analysis system that identifies palindromic sequences from a large genome sequence up to several megabases long. It uses NCBI BLAST as a searching engine, and data processing such as alignment filtration and detection of inverted repeats which satisfy user- defined parameters is performed by manipulating data after populating into a MySQL database. PABAP outperforms publicly available palindrome search program in that it can detect large palindrome with internal spacer at a faster speed from bacterial genomes. It is a standalone application and is freely available for noncommercial users. AVAILABILITY: This application was implemented with free software (Perl, Apache, MySQL, and NCBI BLAST) and is freely available to noncommercial users upon request. Analysis of user data can be carried out directly at http://chimp.kribb.re.kr/~javamint/palindrome.
APACHE
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Filtration
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Genome*
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Genome, Bacterial
2.Human Genome Project.
Journal of the Korean Medical Association 1997;40(12):1680-1686
No abstract available.
Genome, Human*
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Human Genome Project*
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Humans
;
Humans*
3.Post-GWAS Strategies.
Genomics & Informatics 2011;9(1):1-4
Genome-wide association (GWA) studies are the method of choice for discovering loci associated with common diseases. More than a thousand GWA studies have reported successful identification of statistically significant association signals in human genomes for a variety of complex diseases. In this review, I discuss some of the issues related to the future of GWA studies and their biomedical applications.
Genome, Human
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Genome-Wide Association Study
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Humans
4.Analysis of Nuclear Mitochondrial DNA Segments of Nine Plant Species: Size, Distribution, and Insertion Loci.
Genomics & Informatics 2016;14(3):90-95
Nuclear mitochondrial DNA segment (Numt) insertion describes a well-known phenomenon of mitochondrial DNA transfer into a eukaryotic nuclear genome. However, it has not been well understood, especially in plants. Numt insertion patterns vary from species to species in different kingdoms. In this study, the patterns were surveyed in nine plant species, and we found some tip-offs. First, when the mitochondrial genome size is relatively large, the portion of the longer Numt is also larger than the short one. Second, the whole genome duplication event increases the ratio of the shorter Numt portion in the size distribution. Third, Numt insertions are enriched in exon regions. This analysis may be helpful for understanding plant evolution.
DNA, Mitochondrial*
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Exons
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Genome
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Genome, Mitochondrial
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Plants*
5.REPEATOME: A Database for Repeat Element Comparative Analysis in Human and Chimpanzee.
Taeha WOO ; Tae Hui HONG ; Sang Soo KIM ; Won Hyong CHUNG ; Hyo Jin KANG ; Chang Bae KIM ; Jungmin SEO
Genomics & Informatics 2007;5(4):179-187
An increasing number of primate genomes are being sequenced. A direct comparison of repeat elements in human genes and their corresponding chimpanzee orthologs will not only give information on their evolution, but also shed light on the major evolutionary events that shaped our species. We have developed REPEATOME to enable visualization and subsequent comparisons of human and chimpanzee repeat elements. REPEATOME (http://www.repeatome.org/) provides easy access to a complete repeat element map of the human genome, as well as repeat element-associated information. It provides a convenient and effective way to access the repeat elements within or spanning the functional regions in human and chimpanzee genome sequences. REPEATOME includes information to compare repeat elements and gene structures of human genes and their counterparts in chimpanzee. This database can be accessed using comparative search options such as intersection, union, and difference to find lineage-specific or common repeat elements. REPEATOME allows researchers to perform visualization and comparative analysis of repeat elements in human and chimpanzee.
Genome
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Genome, Human
;
Humans*
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Pan troglodytes*
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Primates
6.Genome editing: the road of CRISPR/Cas9 from bench to clinic.
Experimental & Molecular Medicine 2016;48(10):e265-
Molecular scissors engineered for site-specific modification of the genome hold great promise for effective functional analyses of genes, genomes and epigenomes and could improve our understanding of the molecular underpinnings of disease states and facilitate novel therapeutic applications. Several platforms for molecular scissors that enable targeted genome engineering have been developed, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and, most recently, clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated-9 (Cas9). The CRISPR/Cas9 system's simplicity, facile engineering and amenability to multiplexing make it the system of choice for many applications. CRISPR/Cas9 has been used to generate disease models to study genetic diseases. Improvements are urgently needed for various aspects of the CRISPR/Cas9 system, including the system's precision, delivery and control over the outcome of the repair process. Here, we discuss the current status of genome engineering and its implications for the future of biological research and gene therapy.
Genetic Therapy
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Genome*
7.Expression of the S Genome Segment of Hantaan 76-118 in E. coli: Evaluation of Antigenicity of the capsid Protein.
Yun Tai LEE ; Bo Kyung YUN ; Jeong Joong YOON ; Kyoung Won YOUN ; Kyung Hee LEE
Journal of Bacteriology and Virology 2001;31(2):187-192
No abstract available.
Capsid Proteins*
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Capsid*
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Genome*
8.Pathogenesis and Genome of Vibrio parahaemolyticus.
Journal of the Korean Society for Microbiology 2000;35(5):340-342
No Abstract Available.
Genome*
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Vibrio parahaemolyticus*
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Vibrio*
9.Pathogenesis and Genome of Vibrio parahaemolyticus.
Journal of the Korean Society for Microbiology 2000;35(5):340-342
No Abstract Available.
Genome*
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Vibrio parahaemolyticus*
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Vibrio*
10.Historical Meaning of 「Universal Declaration on the Human Genome and Human Right」.
Journal of the Korean Medical Association 1998;41(3):238-239
No abstract available.
Genome, Human*
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Humans
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Humans*