• Genomics & Informatics
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• v.20 no.1
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• pp.3.1-3.10
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• 2022

The recent development of whole-genome sequencing technologies paved the way for understanding the genomes of microorganisms. Every whole-genome sequencing (WGS) project requires a considerable cost and a massive effort to address the questions at hand. The final step of WGS is data analysis. The analysis of whole-genome sequence is dependent on highly sophisticated bioinformatics tools that the research personal have to buy. However, many laboratories and research institutions do not have the bioinformatics capabilities to analyze the genomic data and therefore, are unable to take maximum advantage of whole-genome sequencing. In this aspect, this study provides a guide for research personals on a set of bioinformatics tools available online that can be used to analyze whole-genome sequence data of bacterial genomes. The web interfaces described here have many advantages and, in most cases exempting the need for costly analysis tools and intensive computing resources.

• Food Science of Animal Resources
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• v.35 no.1
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• pp.86-90
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• 2015

In this study, we reported the morphogenetic analysis and genome sequence by genomic analysis of the newly isolated staphylococcal phage SMSAP5 from soil of slaughterhouses for cattle. Based on transmission electron microscopy evident morphology, phage SMSAP5 belonged to the Siphoviridae family. Phage SMSAP5 had a double-stranded DNA genome with a length of 45,552 bp and 33 % G+C content. Bioinformatics analysis of the phage genome revealed 43 open reading frames. A blastn search revealed that its nucleotide sequence shared a high degree of similarity with that of the Staphylococcus phage tp310-2. In conclusion, this study is the first report to show the morphological features and the complete genome sequence of the phage SMSAP5 from soil of slaughterhouses for cattle.

• The Plant Pathology Journal
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• v.17 no.6
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• pp.391.4-391
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• 2001

• Food Science of Animal Resources
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• v.37 no.6
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• pp.884-888
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• 2017

In this study, we report the morphogenetic analysis and genome sequence of a new WCP30 phage of Weissella cibaria, isolated from a fermented food. Based on its morphology, as observed by transmission electron microscopy, WCP30 phage belongs to the family Siphoviridae. Genomic analysis of WCP30 phage showed that it had a 33,697-bp double-stranded DNA genome with 41.2% G+C content. Bioinformatics analysis of the genome revealed 35 open reading frames. A BLASTN search showed that WCP30 phage had low sequence similarity compared to other phages infecting lactic acid bacteria. This is the first report of the morphological features and complete genome sequence of WCP30 phage, which may be useful for controlling the fermentation of dairy foods.

• Molecules and Cells
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• v.22 no.3
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• pp.300-307
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• 2006

Brassica rapa ssp. pekinensis (Chinese cabbage) is an economically important crop and a model plant for studies on polyploidization and phenotypic evolution. To gain an insight into the structure of the B. rapa genome we analyzed 12,017 BAC-end sequences for the presence of transposable elements (TEs), SSRs, centromeric satellite repeats and genes, and similarity to the closely related genome of Arabidopsis thaliana. TEs were estimated to occupy 14% of the genome, with 12.3% of the genome represented by retrotransposons. It was estimated that the B. rapa genome contains 43,000 genes, 1.6 times greater than the genome of A. thaliana. A number of centromeric satellite sequences, representing variations of a 176-bp consensus sequence, were identified. This sequence has undergone rapid evolution within the B. rapa genome and has diverged among the related species of Brassicaceae. A study of SSRs demonstrated a non-random distribution with a greater abundance within predicted intergenic regions. Our results provide an initial characterization of the genome of B. rapa and provide the basis for detailed analysis through whole-genome sequencing.

• Biotechnology and Bioprocess Engineering:BBE
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• v.5 no.3
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• pp.159-163
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• 2000

The genome sequencing project has generated and will contitute to generate enormous amounts of sequence data. Since the first complete genome sequence of bacterium Haemophilus in fluenzae was published in 1995, the complete genome sequences of 2 eukaryotic and about 22 prokaryotic organisms have detemined. Given this everincreasing amounts of sequence information, new strategies are necessary to efficiently pursue the phase of the geome project- the elucidation of gene expression patterns and gene product function on a whole genome scale. In order to assign functional information to the genome sequence, DNA chip technology was developed to efficienfly identify the differential expression pattern of indepondent biogical samples. DNA chip provides a new tool for genome expreesion analysis that may revolutionize revolutionize many aspects of human kife including mew surg discovery and human disease diagnostics.

• Korean Journal of Plant Taxonomy
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• v.52 no.4
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• pp.262-268
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• 2022

The complete chloroplast genome (cp genome) sequence of Clematis calcicola J. S. Kim (Ranunculaceae) is 159,655 bp in length. It consists of large (79,451 bp) and small (18,126 bp) single-copy regions and a pair of identical inverted repeats (31,039 bp). The genome contains 92 protein-coding genes, 36 transfer RNA genes, eight ribosomal RNA genes, and two pseudogenes. A phylogenetic analysis based on the cp genome of 19 taxa showed high similarity between our cp genome and data published for C. calcicola, which is recognized as a species endemic to the Korean Peninsula. The complete cp genome sequence of C. calcicola reported here provides important information for future phylogenetic and evolutionary studies of Ranunculaceae.

• Journal of Korea Multimedia Society
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• v.7 no.3
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• pp.408-417
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• 2004

Genome analysis process requires several steps of various software analysis tools. We propose WGAT(Web-based Genome Analysis Tool), which combines several tools for gene analysis and provides a graphic user interface for users. Software tools related to gene analysis are based on Linux or Unix oriented program, which is difficult to install and use for biologists. Furthermore, files generated from gene analysis frequently require manual transformation for next step input file. Web-based tools which are recently developed process orily one sequence at a time. So it needs many repetitive processes to analyze large size data file. WGAT is developed to support Web-based genome analysis for easy use as well as fast service for users. Whole genome data analysis can be done by running WGAT on Linux server and giving sequence data files with various options. Therefore many steps of the analysis can be done automatically by the system. Simulation shows that WGAT method gives 20 times faster analysis when sequence segment is one thousand.

• Microbiology and Biotechnology Letters
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• v.51 no.3
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• pp.289-292
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• 2023

Thermotolerant Bacillus subtilis NIB353 was isolated from Nuruk, a traditional Korean fermentation starter. The complete B. subtilis NIB353 genome sequence was obtained using MinION and Illumina (MiSeq) platforms. The B. subtilis NIB353 genome sequence was 4,247,447 bp with a GC content of 43%. The B. subtilis NIB353 strain exhibited orthologous average nucleotide identity values of 98.39% and 98.38% with B. subtilis 168 and B. subtilis ATCC6051a, respectively. The genome has been deposited in GenBank under the accession number NZ_CP089148.1.

• Microbiology and Biotechnology Letters
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• v.51 no.1
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• pp.128-131
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• 2023

Here we report the draft genome sequence of Weissella koreensis strain HJ and genomic analysis of its key features. The genome consists of 1,427,571 bp with a GC content of 35.5%, and comprises 1,376 coding genes. In silico analysis revealed the absence of pathogenic factors within the genome. The genome harbors several genes that play an important role in the survival of the gastrointestinal tract. In addition, a type III polyketide synthase cluster was identified. Pangenome analysis identified 68 unique genes in W. koreensis strain HJ. The genome information of this strain provides the basis for understanding its probiotic properties.