• 한국콘텐츠학회:학술대회논문집
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• 한국콘텐츠학회 2018년도 춘계 종합학술대회 논문집
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• pp.553-554
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• 2018

In this study, a user can easily determine the values for a user as well as released plant data and get a dot plot representing Ks and Ka values.

• 한국정보과학회논문지:데이타베이스
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• 제35권2호
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• pp.125-131
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• 2008

새로운 유전체 주석달기와 유전체 진화에 대한 연구를 위해서 올소로그(Ortholog)를 탐지하는 일은 매우 유용하다. 이전에 제안한 연구에서, 우리는 여러 종의 유전체로부터 올소로그 클러스터를 자동적으로 구축하는 방법을 제안하였다. 이 방법은 단지 두 종의 결과를 생성하는 InParanoid를 여러 종으로 확장하고 이와 동일한 질을 가진 결과를 산출한다. 한편, 새롭게 서열이 밝혀진 유전자의 기능을 보다 정확히 예측하기 위해, 패럴로그(Paralog)가 가급적 적게 포함되는 올소로그 클러스터를 구축하는 것이 중요한 문제가 될 수 있다. 이 논문에서, 우리는 임계값을 사용하여 보다 순수한 올소로그 클러스터를 구축하는 방법에 대하여 조사하였다 우리는 20개의 원핵생물의 데이타셋으로부터 올소로그 클러스터를 구축하였다. 우리의 올소로그 클러스터를 COG(Clusters of Orthologous Group) 및 KO(Kegg Orthology)와 비교하였을 매, 약 90%의 유사도를 가지며 임계간의 증가와 더불어 증가하는 경향이 있다.

• Fisheries and Aquatic Sciences
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• 제20권12호
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• pp.31.1-31.11
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• 2017

Background: Liver-expressed antimicrobial peptide-2 (LEAP-2) is an important component of innate immune system in teleosts. In order to understand isoform-specific involvement and regulation of LEAP-2 genes in mud loach (Misgurnus mizolepis, Cypriniformes), a commercially important food fish, this study was aimed to characterize gene structure and expression characteristics of two paralog LEAP-2 isoforms. Results: Mud loach LEAP-2 isoforms (LEAP-2A and LEAP-2B) showed conserved features in the core structure of mature peptides characterized by four Cys residues to form two disulfide bonds. The two paralog isoforms represented a tripartite genomic organization, known as a common structure of vertebrate LEAP-2 genes. Bioinformatic analysis predicted various transcription factor binding motifs in the 5'-flanking regions of mud loach LEAP-2 genes with regard to development and immune response. Mud loach LEAP-2A and LEAP-2B isoforms exhibited different tissue expression patterns and were developmentally regulated. Both isoforms are rapidly modulated toward upregulation during bacterial challenge in an isoform and/or tissue-dependent fashion. Conclusion: Both LEAP-2 isoforms play protective roles not only in embryonic and larval development but also in early immune response to bacterial invasion in mud loach. The regulation pattern of the two isoform genes under basal and stimulated conditions would be isoform-specific, suggestive of a certain degree of functional divergence between isoforms in innate immune system in this species.

• Genomics & Informatics
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• 제7권3호
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• pp.141-147
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• 2009

Developed proteome-scale ortholog and paralog prediction methods are mainly based on sequence similarity. However, it is known that even the closest BLAST hit often does not mean the closest neighbor. For this reason, we added conserved interaction information to find orthologs. We propose a genome-scale, automated ortholog prediction method, named OrthoInterBlast. The method is based on both sequence and interaction similarity. When we applied this method to fly and yeast, 17% of the ortholog candidates were different compared with the results of Inparanoid. By adding protein-protein interaction information, proteins that have low sequence similarity still can be selected as orthologs, which can not be easily detected by sequence homology alone.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.156-160
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• 2005

We introduce a fully automatic clustering method to classier candidate paralog clusters from a set of protein sequences within one genome. A set of protein sequences is represented as a set of nodes, each represented by the amino acid sequence for a protein with the sequence similarities among them constituting a set of edges in a graph of protein relationships. We use graph-based clustering methods to identify structurally consistent sets of nodes which are strongly connected with each other. Our results are consistent with those from current leading systems such as COG/KOG and KEGG based on manual curation. All the results are viewable at http://www.cs.rutgers.edu/${\sim}$seabee.

• Mycobiology
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• 제48권1호
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• pp.44-50
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• 2020

Calonectria pseudonaviculata and C. henricotiae are two closely related fungal species responsible for boxwood blight disease of ornamental shrubs (Buxus spp.) in the U.S. and Europe. A previous study has shown isolates of the latter species, which is restricted to Europe, to be less sensitive to tetraconazole, an azole fungicide. In this study, we have analyzed the CYP51 paralogs for polymorphism in 26 genomes, representing geographically disparate populations of C. pseudonaviculata (n = 19) and C. henricotiae (n = 7), from the U.S., Europe, Asia, and New Zealand. The presence of a CYP51A pseudogene and lack of a functional CYP51A paralog in all C. pseudonaviculata genomes examined is a novel discovery for fungi and could have implications for the evolution of resistance to antifungal chemicals.

• BMB Reports
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• 제51권3호
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• pp.151-156
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• 2018

The Hippo signaling pathway controls nuclear accumulation and stability of the transcriptional coregulator YAP and its paralog TAZ. The activity of Hippo-YAP signaling is influenced not only by biochemical signals, but also by cell shape and mechanical tension transmitted through cell-cell junctions and cell-matrix adhesions. Data accumulated thus far indicates that the actin cytoskeleton is a key mediator of the regulation of Hippo-YAP signaling by means of a variety of biochemical and mechanical cues. In this review, we have outlined the role of actin dynamics and actin-associated proteins in the regulation of Hippo-YAP signaling. In addition, we discuss actin-mediated regulation of YAP/TAZ activity independent of the core Hippo kinases MST and LATS. Although our understanding of the link between Hippo-YAP signaling and the actin cytoskeleton is progressing rapidly, many open questions remain.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2004년도 봄 학술발표논문집 Vol.31 No.1 (B)
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• pp.277-279
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• 2004

생물을 진화적으로 분석할 때, 보전적인 유전자(Conserved gene)득은 기능이 알려지지 못했던 다양한 생물학적 정보를 얻어내는데 유용하게 쓰일 수 있다. 특히 완전히 서열이 밝혀진 지놈(Genome) 데이터로부터 진화적으로 보존적인 유전자 서열의 상동성에 따른 분류를 통한 2차 데이터베이스의 구축은 생물학자들에게 다차원적인 정보를 제공 할 수 있다. 이미 이러한 데이터베이스가 다양한 방법에 따라 구축되었고 생물학자들의 연구에 활용되고 있다. 그러나 기 구축된 데이터베이스들은 생물학자들이 이용하기에 Paralogs의 포함 문제점으로 인해 신뢰성이 떨어지거나 데이터베이스 생성기간이 오래 걸린다는 단전이 있다 본 연구는 기존에 구축된 데이터베이스들의 구축방법을 응용하고, 정보기술을 활용하여 빠르고 효과적으로 정확성을 높인 새로운 구축 방법론과 데이터베이스를 활용한 분석 시스템에 대해 제시하고자 한다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.109-112
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• 2005

Identifying orthologous paralogenes is a fundamental problem in comparative genomics and can facilitate the study of evolutionary history of the species. Existing approaches for locating paralogs make use of local alignment based algorithms such as BLAST. However, there are cases that genes with high alignment scores are not paralogenes. On the other hand, whole genome alignment tools are designed to locate orthologs. Most of these tools are based on some unique substrings (called anchors) in the corresponding orthologous pair to identify them. Intuitively, these tools may not be useful in identifying orthologous paralogenes as paralogenes are very similar and there may not be enough unique anchors. However, our study shows that this is not true. Paralogenes although are similar, they have undergone different mutations. So, there are enough unique anchors for identifying them. Our contributions include the followings. Based on this counter-intuitive finding, we propose to employ the whole genome alignment tools to help verifying paralogenes. Our experiments on five pairs of human-mouse chromosomes show that our approach is effective and can identify most of the mis-classified paralog groups (more than 80%). We verify our finding that whole genome alignment tools are able to locate orthologous paralogenes through a simulation study. The result from the study confirms our finding.

• Parasites, Hosts and Diseases
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• 제41권4호
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• pp.209-219
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• 2003

The evolutionary course of the CsRn1 long-terminal-repeat (LTR) retrotransposon was predicted by conducting a phylogenetic analysis with its paralog LTR sequences. Based on the clustering patterns in the phylogenetic tree, multiple CsRn1 copies could be grouped into four subsets, which were shown to have different integration times. Their differential sequence divergences and heterogeneous integration patterns strongly suggested that these subsets appeared sequentially in the genome of C. sinensis. Members of recently expanding subset showed the lowest level of divergence in their L TR and reverse transcriptase gene sequences. They were also shown to be highly polymorphic among individual genomes of the trematode. The CsRn1 element exhibited a preference for repetitive, agenic chromosomal regions in terms of selecting integration targets. Our results suggested that CsRn1 might induce a considerable degree of intergenomic variation and, thereby, have influenced the evolution of the C. sinensis genome.