• Genomics & Informatics
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• 제20권1호
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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.

• 한국축산식품학회지
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• 제35권1호
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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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• 제17권6호
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• pp.391.4-391
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• 2001

• 한국축산식품학회지
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• 제37권6호
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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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• 제22권3호
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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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• 제5권3호
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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.

• 식물분류학회지
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• 제52권4호
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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.

• 한국멀티미디어학회논문지
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• 제7권3호
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• pp.408-417
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• 2004

유전체 분석 과정은 여러 단계를 걸쳐 다양한 소프트웨어 분석 도구가 사용되는 복잡한 작업을 수반한다. 유전체 분석과 관련된 기존의 소프트웨어 도구들은 대부분 리눅스나 유닉스 기반 프로그램 이므로 생물학자가 이들을 설치하고 사용하는데 어려움과 불편함이 많은 실정이다. 또한, 분석의 각 단계별로 생산되는 파일은 수작업을 통한 변환을 거쳐야만 다음 단계의 입력으로 사용될 수 있다. 근래에 웹을 기반으로한 도구들이 개발되고 있으나 한번에 하나의 서열을 처리하는 방식이므로 대량의 실험 데이터를 분석하는 경우에는 반복 작업으로 인한 시간과 노력이 요구되는 단점을 갖고 있다. 본 논문에서는 유전체 분석에 필요한 여러 도구들을 웹 환경에서 하나의 그래픽 사용자 인터페이스로 통합하여 생물학자들이 보다 쉽게 서열과 기능을 분석할 수 있도록 한 WGAT(Web-based Genome Analysis Tool)를 제안한다. WGAT는 리눅스 서버에 유전체 데이터 분석프로그램을 구동하고, 클라이언트 웹 (web)에서 데이터 파일과 분석에 필요한 선택사항들을 입력함으로써 한번에 여러 단계의 분석 작업을 수작업 없이 자동으로 처리할 수 있다. WGAT시스템의 생산성을 분석하기 위하여 기존의 방식과 WGAT를 이용한 방식의 서열분석 처리 시간을 비교한 결과 서열 단편의 개수가 1000개인 경우 기존의 방식보다 20배 이상 분석 능력이 향상됨을 확인할 수 있었다.

• 한국미생물·생명공학회지
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• 제51권3호
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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.

• 한국미생물·생명공학회지
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• 제51권1호
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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.