• BMB Reports
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• 제49권12호
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• pp.653-654
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• 2016

The human reference genome, maintained by the Genome Reference Consortium, is conceivably the most complete genome assembly ever, since its first construction. It has continually been improved by incorporating corrections made to the previous assemblies, thanks to various technological advances. Many currently-ongoing population sequencing projects have been based on this reference genome, heightening hopes of the development of useful medical applications of genomic information, thanks to the recent maturation of high-throughput sequencing technologies. However, just one reference genome does not fit all the populations across the globe, because of the large diversity in genomic structures and technical limitations inherent to short read sequencing methods. The recent success in de novo construction of the highly contiguous Asian diploid genome AK1, by combining single molecule technologies with routine sequencing data without resorting to traditional clone-by-clone sequencing and physical mapping, reveals the nature of genomic structure variation by detecting thousands of novel structural variations and by finally filling in some of the prior gaps which had persistently remained in the current human reference genome. Now it is expected that the AK1 genome, soon to be paired with more upcoming de novo assembled genomes, will provide a chance to explore what it is really like to use ancestry-specific reference genomes instead of hg19/hg38 for population genomics. This is a major step towards the furthering of genetically-based precision medicine.

• 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.

• BMB Reports
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• 제39권3호
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• pp.240-246
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• 2006

The base compositional correlations that hold among various coding and noncoding regions of the canine genome have been analysed. The distribution pattern of genes, on the basis of $GC_3$ composition, shows a wide range similar to that observed in human. However the occurrence of maximum number of genes was observed in the range of 65-75% of $GC_3$ composition. The correlation between the coding DNA sequences of canine with the different noncoding regions (introns and flanking regions) is found to be significant and in many cases the degree of correlation show similarity to human genome. We found that these correlations are not limited to the GC content alone, but is holding at the level of the frequency of individual bases as well. The present study suggests that canines ideally belong to the predicted 'general mammalian pattern' of genome composition along with human beings.

• 생명과학회지
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• 제18권4호
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• pp.572-579
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• 2008

경제 동물의 유전체 연구는 최근에 급속하게 발전하여 초기의 유전체 지도로 부터 유전자의 발견에 필수적인 앙적/질적 형질 유전자를 확인 동정가능한 수준의 지도가 개발되었다. 이러한 발전은 경제동물의 전체 게놈 염기서열 결정과 대량 ESTs의 개발에 의해 가능해졌다. 특히 염시서열 결정은 경제형질과 연관된 대규모의 SNPs 개발에 의한 QTL 연구에 유용한 정보를 제공할 것으로 사료된다. 비교 유전체 연구를 통해 인간 및 설치류 모델동물에서 나온 유전체 정보를 이용하여 경제 동물의 유전체 연구에 있어 중요한 발견을 이루었다. 이러한 노력은 좀더 밀도 높은 QTL지도의 작성을 가능하게 하여 쉽게 측정하기 어려운 경제형질과 연관된 유전자의 확인 및 동정을 가능하게 하고 궁극적으로 산업체에서 이용 가능한 표지인자의 개발을 가능하게 할 것으로 사료된다. 이와 더불어, 경제동물 유전체 연구 성과는 인간의 생리현상의 유전체 측면의 이해를 더욱 증진시킬 것이다.

• BMB Reports
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• 제41권4호
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• pp.287-293
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• 2008

In a yeast two-hybrid screen, we identified the microtubule-destabilizing protein SCG10 as a potential effector protein of $BRI_3$. The association was verified using GST pull-down, Co-IP, and their perinuclear co-localization. The analysis of in vitro microtubule polymerization/depolymerization showed that the binding of $BRI_3$ to SCG10 effectively blocked the ability of SCG10 to induce microtubule disassembly, as determined by turbidimetric assays. In intact PC12 cells, $BRI_3$ exhibited the ability to stabilize the microtubule network and attenuate the microtubule-destabilizing activity of SCG10. Furthermore, co-expression of $BRI_3$ with SCG10 attenuated SCG10-mediated PC12 cell neurite outgrowth induced by NGF. These results identify a novel connection between a neuron-specific BRI protein and the cytoskeletal network, suggesting possible roles of BRI3 in the process of neuronal differentiation.

• 미생물학회지
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• 제54권1호
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• pp.74-76
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• 2018

최근 Fusobacterium nucleatum subsp. vincentii는 average nucleotide identity 및 genome-to-genome distance 분석법에 의해 Fusobacterium vincentii로 재분류 되었다. F. vincentii는 그람 음성이면서, 혐기성 및 가는 섬유 모양의 세균이다. F. vincentii는 사람의 구강 내 정상세균총의 하나이고, 치주질환에 중요한 역할을 한다. F. vincentii KCOM 2931 균주가 사람 치주염 병소에서 분리되었다. F. vincentii KCOM 2931 균주 유전체 염기서열을 해독하여 보고한다.

• 미생물학회지
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• 제54권1호
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• pp.71-73
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• 2018

최근 Fusobacterium nucleatum subsp. polymorphum는 average nucleotide identity 및 genome-to-genome distance 분석법에 의해 Fusobacterium polymorphum로 재분류 되었다. F. polymorphum 그람 음성이면서, 혐기성 및 가는 섬유 모양의 세균이다. F. polymorphum은 사람의 구강 내 정상세균총의 하나이고, 치주질환의 원인 인자이다. F. polymorphum KCOM 1001 (= ChDC F119) 균주가 사람 치은염 병소의 치은연하치면세균막에서 분리되었다. F. polymorphum KCOM 1001 균주 유전체 염기서열을 해독하여 보고한다.

• Genomics & Informatics
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• 제4권1호
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• pp.45-47
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• 2006

D2GSNP is a web-based server for the selection of single nucleotide polymorph isms (SNPs) within genes related to human diseases. The D2GSNP is based on a relational database created by downloading and parsing OMIM, GAD, and dbSNP, and merging it with positional information of UCSC Golden Path. Totally our server provides 5,142 and 1,932 non-redundant disease genes from OMIM and GAD, respectively. With the D2GSNP web interface, users can select SNPs within genes responding to certain diseases and get their flanking sequences for further genotyping experiments such as association studies.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2002년도 제1차워크샵
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• pp.105-121
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• 2002

최근 인간 지놈(genome)의 DNA가 밝혀져서 많은 관심을 받았는데, 이를 수행하는 방법을 소개한다. Human Genome Project에서 채택한 BAC-to-BAC 방식과 Celera 회사에서 채택한 whole genome shotgun 방식을 설명한다. 또한 두 방식에서 공히 fragment assembly 프로그램을 사용하는데, 이 프로그램의 개요를 설명한다.

• 한국유전체학회:학술대회논문집
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• 한국유전체학회 2002년도 The 11th Korea Genome Conference
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• pp.28-28
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• 2002