• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.78-82
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• 2005

Three of the genus Pseudomonas (P. aeruginosa, P. putida, P. syringae) show highly different phenotypic characteristics among them. Two of the three members are pathogenic and the other is non-pathogenic. Comparative analyses of the complete genomes can elucidate the genomic similarities and differences among them. We analyzed the three genomes and the genes of them to reveal the degree of conservation of chromosomes and similarity of the genes. The 2-dimensional dot plot between the pathogenic P. aeruginosa and non-pathogenic P. putida shared higher portion of the nucleotide sequences than other two combinations. Comparison of the nucleotide compositions by calculating the genome-scale plot of G+C contents and GC skew showed the variation of location. Comparison of the metabolic capabilities using the functional classification of KEGG orthology revealed that the differences in the number of genes for the specific functional categories resulted in the phenotypic differences. Finally combination of the analyses using the protein homologs supported the evolutionary distance of the P. putida obtained from other genome-scale comparisons.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.113-117
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• 2005

In comparative genome analyses, synteny blocks play important roles for finding ortholog genes, reconstructing phylogenetic tree and predicting genome rearrangement events. In this paper, we propose a novel method to search biologically plausible synteny blocks not only from the viewpoint of finding highly preserved regions but also from the viewpoint of analyzing genome rearrangements. We have applied the method to our experiments on four fungal organisms, and succeeded to obtain some biologically interesting results.

• 통합자연과학논문집
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• 제7권3호
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• pp.166-172
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• 2014

Caspases, a family of cysteinyl aspartate-specific proteases plays a central role in the regulation and the execution of apoptotic cell death. Activation of caspases-3 stimulates a signaling pathway that ultimately leads to the death of the cell. Hence, caspase-3 has been proven to be an effective target for reducing the amount of cellular and tissue damage. In this work, comparative molecular field analysis (CoMFA) was performed on a series of 3, 4-dihydropyrimidoindolones derivatives which are inhibitors of caspase-3. The best predictions were obtained for CoMFA model ($q^2=0.676$, $r^2=0.990$). The predictive ability of test set ($r^2_{pred}$) was 0.688. Statistical parameters from the generated QSAR models indicated the data is well fitted and have high predictive ability. Our theoretical results could be useful to design novel and more potent caspase-3 derivatives.

• BMB Reports
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• 제42권12호
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• pp.823-828
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• 2009

Techniques for analyzing protein-DNA interactions on a genome-wide scale have recently established regulatory roles for distal enhancers. However, the large sizes of higher eukaryotic genomes have made identification of these elements difficult. Information regarding sequence conservation, exon annotation and repetitive regions can be used to reduce the size of the search region. However, previously developed resources are inadequate for consolidating such information. CONVIRT is a web resource for the identification of transcription factor binding sites and also features comparative genomics. Genomic information on ortholog-independent conserved regions, exons, repeats and sequences is integrated into the virtual chromosome, and statistically over-represented single or combinations of transcription factor binding sites are sought. CONVIRT provides regulatory network analysis for several organisms with long promoter regions and permits inter-species genome alignments. CONVIRT is freely available at http://biosoft.kaist.ac.kr/convirt.

• 통합자연과학논문집
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• 제9권4호
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• pp.241-248
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• 2016

Corticotropin-releasing factor receptors (CRFRs) activate the hypothalamic-pituitary-adrenal axis, which is an integral part of the fight or flight response to stress. Increase in CRH level is observed in Alzheimer's disease and major depression and hypoglycemia. Here, we report on the relevant physicochemical parameters required for the CRFR inhibitors. Comparative molecular similarity indices analysis (CoMSIA) was performed with the derivatives of 8-substituted-2-aryl-5-alkylaminoquinolinesas CRFR inhibitors. The best predictions were obtained for the best CoMSIA model with a $q^2$ of 0.576 with 6 components and $r^2$ of 0.977. The statistical parameters from the generated CoMSIA models indicated that the data are well fitted and have high predictive ability. CoMSIA contour maps could be useful in the designing of more potent and novel CRFR derivatives.

• 통합자연과학논문집
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• 제7권4호
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• pp.227-233
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• 2014

Caspases, a family of cysteinyl aspartate-specific proteases plays a central role in the regulation and the execution of apoptotic cell death. Activation of caspases-3 stimulates a signaling pathway that ultimately leads to the death of the cell. Hence, caspase-3 has been proven to be an effective target for reducing the amount of cellular and tissue damage. In this work, comparative molecular similarity indices analysis (CoMSIA) was performed on a series of 3,4-dihydropyrimidoindolones derivatives which are inhibitors of caspase-3. The best predictions were obtained for CoMSIA model ($q^2$ = 0.586, $r^2$ = 0.955). The predictive ability of test set ($r^2_{pred}$) was 0.723. Statistical parameters from the generated QSAR models indicated the data is well fitted and have high predictive ability. Our theoretical results could be useful to design novel and more potent caspase-3 derivatives.

• Genomics & Informatics
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• 제21권4호
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• pp.49.1-49.11
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• 2023

Recent advances in sequencing technologies and platforms have enabled to generate metagenomics sequences using different sequencing platforms. In this study, we analyzed and compared shotgun metagenomic sequences generated by HiSeq3000 and BGISEQ-500 platforms from 12 sediment samples collected across the Norwegian coast. Metagenomics DNA sequences were normalized to an equal number of bases for both platforms and further evaluated by using different taxonomic classifiers, reference databases, and assemblers. Normalized BGISEQ-500 sequences retained more reads and base counts after preprocessing, while a slightly higher fraction of HiSeq3000 sequences were taxonomically classified. Kaiju classified a higher percentage of reads relative to Kraken2 for both platforms, and comparison of reference database for taxonomic classification showed that MAR database outperformed RefSeq. Assembly using MEGAHIT produced longer assemblies and higher total contigs count in majority of HiSeq3000 samples than using metaSPAdes, but the assembly statistics notably improved with unprocessed or normalized reads. Our results indicate that both platforms perform comparably in terms of the percentage of taxonomically classified reads and assembled contig statistics for metagenomics samples. This study provides valuable insights for researchers in selecting an appropriate sequencing platform and bioinformatics pipeline for their metagenomics studies.

• Asian-Australasian Journal of Animal Sciences
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• 제23권11호
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• pp.1399-1404
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• 2010

We have created a Bovine Genome Database, an integrated genomic resource for Bos taurus, by merging bovine data from various databases and our own data. We produced 55,213 Korean cattle (Hanwoo) ESTs from cDNA libraries from three tissues. We concentrated on genomic information based on Hanwoo transcripts and provided user-friendly search interfaces within the Bovine Genome Database. The genome browser supported alignment results for the various types of data: Hanwoo EST, consensus sequence, human gene, and predicted bovine genes. The database also provides transcript data information, gene annotation, genomic location, sequence and tissue distribution. Users can also explore bovine disease genes based on comparative mapping of homologous genes and can conduct searches centered on genes within user-selected quantitative trait loci (QTL) regions. The Bovine Genome Database can be accessed at http://bgd.nabc.go.kr.

• International journal of advanced smart convergence
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• 제9권1호
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• pp.90-97
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• 2020

Oncolytic viruses are characterized by their ability to selectively kill cancer cells, and thus they have potential for application as novel anticancer agents. Despite an increase in the number of studies on methodologies involving oncolytic viruses, bioinformatic studies generating useful data are lacking. We constructed a database for oncolytic virus research (the oncolytic virus database, OVDB) by integrating scattered genetic information on oncolytic viruses and proposed a systematic means of using the biological data in the database. Our database provides data on 14 oncolytic viral strains and other types of viruses for comparative analysis. We constructed the OVDB using the basic local alignment search tool, and therefore can provides genetic information on highly homologous oncolytic viruses. This study contributes to facilitate systematic bioinformatics research, providing valuable data for development of oncolytic virus-based anticancer therapies.

• 한국생명과학회:학술대회논문집
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• 한국생명과학회 2003년도 제39회 학술심포지움
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• pp.89-89
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• 2003