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Genome Sequence of Leuconostoc argentinum KCTC 3773
Nam, Seong-Hyeuk,Choi, Sang-Haeng,Kang, Aram,Kim, Dong-Wook,Kim, Ryong Nam,Kim, Aeri,Park, Hong-Seog American Society for Microbiology 2010 Journal of Bacteriology Vol.192 No.24
<B>ABSTRACT</B><P><I>Leuconostoc argentinum</I> is one of the most prevalent lactic acid bacteria present during the manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome sequence of type strain KCTC 3773 of <I>Leuconostoc argentinum</I> (1,720,683 bp, with a G+C content of 42.9%), which consists of 98 large contigs (>100 bp in size).</P>
PESTAS: a web server for EST analysis and sequence mining.
Nam, Seong-Hyeuk,Kim, Dae-Won,Jung, Tae-Sung,Choi, Young-Sang,Kim, Dong-Wook,Choi, Han-Suk,Choi, Sang-Haeng,Park, Hong-Seog Oxford University Press 2009 Bioinformatics Vol.25 No.14
<P>We have developed a web server for the high-throughput annotation of expressed sequence tags (ESTs) called pipeline for EST analysis service (PESTAS). PESTAS processes entire datasets with an automated pipeline of 13 analytic services, then deposits the data into the MySQL database and transforms it into three kinds of reports: preprocessing, assembling and annotation. All annotated information is provided to the scientist and can be downloaded through a web browser. To get more relevant functional annotation results, a curation function was introduced with which biologists can easily change the best-hit annotation information. We included a gene chip module that detects gene expression differences between libraries by comparing accession number counts from BLAST search results. PESTAS also provides access to the pathway information of KEGG, which is useful for mapping the relationships among networks of annotated enzymes, and is especially valuable for those researchers interested in biological pathways.</P>
남성혁(Seong-Hyeuk Nam),정태성(Tae-Sung Jung),김태경(Tae-Kyung Kim),유재수(Jae-Soo Yoo),조완섭(Wan-Sup Cho) 한국정보과학회 2007 한국정보과학회 학술발표논문집 Vol.34 No.2B
서열을 분석하고, 기능을 예측하는 서열 주해는 생명 현상 규명을 위한 필수 과정이다. 서열 주해는 다수 응용 프로그램간 상호 연계를 통한 복잡한 처리 과정을 거쳐 이루어진다. 현재 사용자는 다양한 응용 프로그램들 중 적합한 응용 프로그램을 선택한 후, 운영환경에 맞도록 설치하고, 사용법을 익혀야 한다. 또한 각 프로그램들의 연계를 위해 입출력 데이터 형식을 변환해야 하는 불편함이 있다. 이를 위해 자동화된 솔루션들이 개발되고 있지만, 각 단계별 프로그램들이 강결합(tightly coupled)되어 있어 유연성(flexibility)이 떨어지고, 기능의 확장 및 변경에 어려움이 있다. 본 논문에서는 기존 시스템들의 한계를 극복하기 위하여 SOA (Service Oriented Architecture) 기반의 서열 주해 시스템인 SeqWeB을 제안한다. SeqWeB은 서열 주해에 필요한 7개의 응용 프로그램(Phred, cross_match, RepeatMasker, ICAtools, Phrap, CAP3, Blast)들을 웹 서비스 기술을 통해 단위 서비스로 개발하고, BPM 기법을 이용하여 통합하였다. SeqWeB은 각 응용 프로그램간 상호 운용성을 높이기 위하여 XML 형식의 입/출력 데이터를 사용하며, SOA 기반의 시스템 통합으로 각 응용 프로그램들을 약결합(loosely coupled)하여 시스템의 확장 및 변경이 용이하다. 또한 웹을 기반으로 하는 다양한 조합의 서열주해 솔루션 제공이 가능한 특징이 있다.
남성혁(Seong-Hyeuk Nam),김태경(Tae-Kyung Kim),김경란(Kyoung-Ran Kim),조완섭(Wan-Sup Cho) 한국컴퓨터정보학회 2008 韓國컴퓨터情報學會論文誌 Vol.13 No.3
본 논문에서는 SOA 기반의 EST 서열 주해 시스템인 SeqWeB을 제안한다. SeqWeB은 EST 서열 주해에 사용되는 8개의 분석 프로그램 (Phrap, cross_match, RepeatMasker, ICAtools, TGICL, CAP 3, Phrap, BLAST)을 웹 서비스로 제작하고, BPEL (Business Process Execution Language)을 통해 8개의 서비스를 다양한 형태로 조합한다. BPEL로 조합한 서비스들은 표준 데이터 형식으로 통신하여 통합 시 상호 운용성을 보장한다. SeqWeB은 웹 서비스와 BPEL을 통한 약 결합 방식으로 통합하여, 기존의 애플리케이션 통합 방식보다 시스템의 확장과 수정이 쉬우며 유지보수 비용이 저렴하다. 또한, SeqWeB은 다른 서비스의 컴포넌트로 사용될 수도 있다. SeqWeB을 통해 SOA가 지향하는 재사용성(Reusability)과 유연성 (Flexible)을 기반으로 기존과 다른 방식의 생물학 분야의 애플리케이션 통합방법론을 제시한다. In this paper, we present an EST sequence annotation system based on Service Oriented Architecture, called SeqWeB. We developed the web services of eight applications (Phred, cross_match, RepeatMasker, TGICL, ICAtools, CAP3, Phrap and Blast) which are located in sequence annotation process and integrated the web services through BFEL. SeqWeB uses an XML file format for data input and output to maximize interoperability between each application. SeqWeB can be extended or modified easily through some modification such as insertion, deletion and replacement because service-oriented architecture allows loose coupling between applications.
Complete Genome Sequence of Halalkalicoccus jeotgali B3T, an Extremely Halophilic Archaeon
Roh, Seong Woon,Nam, Young-Do,Nam, Seong-Hyeuk,Choi, Sang-Haeng,Park, Hong-Seog,Bae, Jin-Woo American Society for Microbiology 2010 Journal of Bacteriology Vol.192 No.17
<B>ABSTRACT</B><P><I>Halalkalicoccus jeotgali</I> B3<SUP>T</SUP>, isolated from salt-fermented seafood from South Korea, is an extremely halophilic archaeon belonging to the family <I>Halobacteriaceae</I>. Here, we present the complete genome sequence of the type strain <I>H. jeotgali</I> B3<SUP>T</SUP> (3,698,650 bp, with a G+C content of 62.5%), which consists of one chromosome and six plasmids. This is the first complete genome sequence of the <I>Halalkalicoccus</I> species.</P>
Novel mechanism of conjoined gene formation in the human genome.
Kim, Ryong Nam,Kim, Aeri,Choi, Sang-Haeng,Kim, Dae-Soo,Nam, Seong-Hyeuk,Kim, Dae-Won,Kim, Dong-Wook,Kang, Aram,Kim, Min-Young,Park, Kun-Hyang,Yoon, Byoung-Ha,Lee, Kang Seon,Park, Hong-Seog Springer 2012 Functional & integrative genomics Vol.12 No.1
<P>Recently, conjoined genes (CGs) have emerged as important genetic factors necessary for understanding the human genome. However, their formation mechanism and precise structures have remained mysterious. Based on a detailed structural analysis of 57 human CG transcript variants (CGTVs, discovered in this study) and all (833) known CGs in the human genome, we discovered that the poly(A) signal site from the upstream parent gene region is completely removed via the skipping or truncation of the final exon; consequently, CG transcription is terminated at the poly(A) signal site of the downstream parent gene. This result led us to propose a novel mechanism of CG formation: the complete removal of the poly(A) signal site from the upstream parent gene is a prerequisite for the CG transcriptional machinery to continue transcribing uninterrupted into the intergenic region and downstream parent gene. The removal of the poly(A) signal sequence from the upstream gene region appears to be caused by a deletion or truncation mutation in the human genome rather than post-transcriptional trans-splicing events. With respect to the characteristics of CG sequence structures, we found that intergenic regions are hot spots for novel exon creation during CGTV formation and that exons farther from the intergenic regions are more highly conserved in the CGTVs. Interestingly, many novel exons newly created within the intergenic and intragenic regions originated from transposable element sequences. Additionally, the CGTVs showed tumor tissue-biased expression. In conclusion, our study provides novel insights into the CG formation mechanism and expands the present concepts of the genetic structural landscape, gene regulation, and gene formation mechanisms in the human genome.</P>
Genome Analysis of the Domestic Dog (Korean Jindo) by Massively Parallel Sequencing
Kim, Ryong Nam,Kim, Dae-Soo,Choi, Sang-Haeng,Yoon, Byoung-Ha,Kang, Aram,Nam, Seong-Hyeuk,Kim, Dong-Wook,Kim, Jong-Joo,Ha, Ji-Hong,Toyoda, Atsushi,Fujiyama, Asao,Kim, Aeri,Kim, Min-Young,Park, Kun-Hyan Oxford University Press 2012 DNA research Vol.19 No.3
<P>Although pioneering sequencing projects have shed light on the boxer and poodle genomes, a number of challenges need to be met before the sequencing and annotation of the dog genome can be considered complete. Here, we present the DNA sequence of the Jindo dog genome, sequenced to 45-fold average coverage using Illumina massively parallel sequencing technology. A comparison of the sequence to the reference boxer genome led to the identification of 4 675 437 single nucleotide polymorphisms (SNPs, including 3 346 058 novel SNPs), 71 642 indels and 8131 structural variations. Of these, 339 non-synonymous SNPs and 3 indels are located within coding sequences (CDS). In particular, 3 non-synonymous SNPs and a 26-bp deletion occur in the <I>TCOF1</I> locus, implying that the difference observed in cranial facial morphology between Jindo and boxer dogs might be influenced by those variations. Through the annotation of the Jindo olfactory receptor gene family, we found 2 unique olfactory receptor genes and 236 olfactory receptor genes harbouring non-synonymous homozygous SNPs that are likely to affect smelling capability. In addition, we determined the DNA sequence of the Jindo dog mitochondrial genome and identified Jindo dog-specific mtDNA genotypes. This Jindo genome data upgrade our understanding of dog genomic architecture and will be a very valuable resource for investigating not only dog genetics and genomics but also human and dog disease genetics and comparative genomics.</P>
Major chimpanzee-specific structural changes in sperm development-associated genes
Kim, Ryong Nam,Kim, Dae-Won,Choi, Sang-Haeng,Chae, Sung-Hwa,Nam, Seong-Hyeuk,Kim, Dong-Wook,Kim, Aeri,Kang, Aram,Park, Kun-Hyang,Lee, Yong Seok,Hirai, Momoki,Suzuki, Yutaka,Sugano, Sumio,Hashimoto, Ka Springer-Verlag 2011 Functional & integrative genomics Vol.11 No.3
Kang, Yeeok,Nam, Seong-Hyeuk,Park, Kyung Sun,Kim, Yoonjung,Kim, Jong-Won,Lee, Eunjung,Ko, Jung Min,Lee, Kyung-A,Park, Inho BioMed Central 2018 BMC bioinformatics Vol.19 No.-
<P><B>Background</B></P><P>Targeted next-generation sequencing (NGS) is increasingly being adopted in clinical laboratories for genomic diagnostic tests.</P><P><B>Results</B></P><P>We developed a new computational method, DeviCNV, intended for the detection of exon-level copy number variants (CNVs) in targeted NGS data. DeviCNV builds linear regression models with bootstrapping for every probe to capture the relationship between read depth of an individual probe and the median of read depth values of all probes in the sample. From the regression models, it estimates the read depth ratio of the observed and predicted read depth with confidence interval for each probe which is applied to a circular binary segmentation (CBS) algorithm to obtain CNV candidates. Then, it assigns confidence scores to those candidates based on the reliability and strength of the CNV signals inferred from the read depth ratios of the probes within them. Finally, it also provides gene-centric plots with confidence levels of CNV candidates for visual inspection. We applied DeviCNV to targeted NGS data generated for newborn screening and demonstrated its ability to detect novel pathogenic CNVs from clinical samples.</P><P><B>Conclusions</B></P><P>We propose a new pragmatic method for detecting CNVs in targeted NGS data with an intuitive visualization and a systematic method to assign confidence scores for candidate CNVs. Since DeviCNV was developed for use in clinical diagnosis, sensitivity is increased by the detection of exon-level CNVs.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (10.1186/s12859-018-2409-6) contains supplementary material, which is available to authorized users.</P>