• Korean Journal of Veterinary Service
• /
• v.39 no.1
• /
• pp.41-49
• /
• 2016

In the present study, fast and robust methods for the next generation sequencing (NGS) were developed for analysis of PRRSV full genome sequences, which is a positive sensed RNA virus with a high degree of genetic variability among isolates. Two strains of PRRSVs (VR2332 and VR2332-R) which have been maintained in our laboratory were used to validate our methods and to compare with the sequence registered in GenBank (GenBank accession no. EF536003). The results suggested that both of strains had 100% coverage with the reference; the VR2332 had the coverage depth from minimum 3 to maximum 23,012, for the VR2332-R from minimum 3 to maximum 41,348, and 22,712 as an average depth. Genomic data produced from the massive sequencing capacities of the NGS have enabled the study of PRRSV at an unprecedented rate and details. Unlike conventional sequence methods which require the knowledge of conserved regions, the NGS allows de novo assembly of the full viral genomes. Therefore, our results suggested that these methods using the NGS massively facilitate the generation of more full genome PRRSV sequences locally as well as nationally in regard of saving time and cost.

• Journal of Animal Environmental Science
• /
• v.21 no.3
• /
• pp.93-98
• /
• 2015

The objective of this study was to review application of next-generation sequencing (NGS) to investigate microbiome in the livestock sector. Since the 16S rRNA gene is used as a phylogenetic marker, unculturable members of microbiome in nature or managed environments have been investigated using the NGS technique based on 16S rRNA genes. However, few NGS studies have been conducted to investigate microbiome in the livestock sector. The 16S rRNA gene sequences obtained from NGS are classified to microbial taxa against the 16S rRNA gene reference database such as RDP, Greengenes and Silva databases. The sequences also are clustered into species-level OTUs at 97% sequence similarity. Microbiome similarity among treatment groups is visualized using principal coordinates analysis, while microbiome shared among treatment groups is visualized using a venn diagram. The use of the NGS technique will contribute to elucidating roles of microbiome in the livestock sector.

• Proceedings of the Korean Information Science Society Conference
• /
• 2011.06b
• /
• pp.466-469
• /
• 2011

최근에 등장한 Next Generation Sequencing(NGS)은 전통적인 방법에 비해 빠르고 저비용으로 대용량의 시퀀스 데이터를 이용한 차세대 시퀀싱 기술을 말한다. 이렇게 얻은 NGS 데이터를 분석하는 단계 중에서 alignment 단계는 시퀀서에서 얻은 대량의 read를 참조 염기서열에 맵핑하는 단계로 NGS 데이터 분석의 가장 기본이면서 핵심인 단계이다. alignment 도구는 긴 참조 염기서열을 색인화해서 짧은 read를 빠르게 맵핑하는 용도로 사용된다. 현재 많이 사용되고 있는 일반적인 alignment 도구들은 입력데이터에 대한 별도의 전처리 과정이 없으며 나열된 read를 순차적으로 맵핑하는 단순한 구조를 가지고 있다. 본 논문은 NGS 데이터의 특징 중에 특히 read간의 중복성이 존재하고 이를 이용한 read의 효율적 공통부분 서열을 찾는다. 중복이 가능한 read의 공통부분서열과 read의 관계를 그래프 이론의 Hitting Set 문제로 모델링하고 여러 read가 포함하는 공통 부분서열을 사용해서 alignment 단계의 효율을 높일 수 방법을 제안한다.

• Journal of Educational Research in Mathematics
• /
• v.17 no.2
• /
• pp.179-199
• /
• 2007

The purpose of this study was to discover differences between mathematically gifted students (MGS) and non-gifted students (NGS) when making probability judgments. For this purpose, the following research questions were selected: 1. How do MGS differ from NGS when making probability judgments(answer correctness, answer confidence)? 2. When tackling probability problems, what effect do differences in probability judgment factors have? To solve these research questions, this study employed a survey and interview type investigation. A probability test program was developed to investigate the first research question, and the second research question was addressed by interviews regarding the Program. Analysis of collected data revealed the following results. First, both MGS and NGS justified their answers using six probability judgment factors: mathematical knowledge, use of logical reasoning, experience, phenomenon of chance, intuition, and problem understanding ability. Second, MGS produced more correct answers than NGS, and MGS also had higher confidence that answers were right. Third, in case of MGS, mathematical knowledge and logical reasoning usage were the main factors of probability judgment, but the main factors for NGS were use of logical reasoning, phenomenon of chance and intuition. From findings the following conclusions were obtained. First, MGS employ different factors from NGS when making probability judgments. This suggests that MGS may be more intellectual than NGS, because MGS could easily adopt probability subject matter, something not learnt until later in school, into their mathematical schemata. Second, probability learning could be taught earlier than the current elementary curriculum requires. Lastly, NGS need reassurance from educators that they can understand and accumulate mathematical reasoning.

• KIISE Transactions on Computing Practices
• /
• v.20 no.9
• /
• pp.513-518
• /
• 2014

It has become possible for small scale laboratories to interpret large scale genomic DNA, thanks to the reduction of the sequencing cost by the development of next generation sequencing (NGS). De novo assembly is a method which creates a putative original sequence by reconstructing reads without using a reference sequence. There have been various study results on de novo assembly, however, it is still difficult to get the desired results even by using the same assembly procedures and the analysis tools which were suggested in the studies reported. This is mainly because there are no specific guidelines for the assembly procedures or know-hows for the use of such analysis tools. In this study, to resolve these problems, we introduce steps to finding whole genome of an unknown DNA via NGS technology and de novo assembly, while providing the pros and cons of the various analysis tools used in each step. We used 350Mbp of Toxocara canis DNA as an application case for the detailed explanations of each stated step. We also extend our works for prediction of protein-coding genes and their functions from the draft genome sequence by comparing its homology with reference sequences of other nematodes.

• Journal of The Korean Society of Inherited Metabolic disease
• /
• v.23 no.2
• /
• pp.1-7
• /
• 2023

Inherited metabolic disorders (IMD) are a group of disorders involving various metabolic pathways. Genetic diagnosis of IMD has been challenging because of extremely heterogeneous nature and extensive laboratory and/or phenotype overlap. Conventional genetic diagnosis was a gene-by-gene approach that needs a priori information on the causative genes that might underlie the IMD. Recent implementation of next-generation sequencing (NGS) technologies has changed the process of genetic diagnosis from a gene-by-gene approach to simultaneous analysis of targeted genes possibly associated with the IMD using gene panels or using whole exome/genome sequencing (WES/WGS) covering entire human genes. Clinical NGS tests can be a cost-effective approach for the rapid diagnosis of IMD with genetic heterogeneity and are becoming standard diagnostic procedures.

• The Korean Journal of Malacology
• /
• v.32 no.3
• /
• pp.185-188
• /
• 2016

PANM-DB (version 1.0) was constructed as a web-based interface for the analysis and annotation of Next-Generation Sequencing (NGS) data of Mollusca, Arthropoda, and Nematoda. The database collected the sequences of Protostomes (Mollusca, Arthropoda, and Nematoda) from the NCBI Taxonomy Browser, and the same were compiled in a multi-FASTA format and stored using the formatdb program. This improved the processing of the RNA-seq sequences in terms of speed and hit percentage. PANM-DB has been successfully used for the transcriptome annotation of butterfly, land snail, and other commercial mollusca. We have improved the database by updating the same with new sequences and version 2.0 contains a total of 7,571,246 protein sequences (two times more as compared to version 1.0). Furthermore, the updated version contains the Cephalopoda database. The constructed web interface is available that independently analyses following these updates that is an improvement of the mollusks BLAST server. The updated version of PANM-DB will be helpful for the analysis of the NGS based sequencing data of non-model species, especially Mollusca, Arthropoda, Nematoda.

• Korean Journal of Veterinary Service
• /
• v.42 no.4
• /
• pp.217-225
• /
• 2019

To detect Single nucleotide polymorphisms (SNP) markers associated with Bovine viral diarrhea virus (BVDV) and Bovine respiratory syncytial virus (BRSV) S/P ratio in Korean Holstein dairy cattle, Genome-wide association study (GWAS) was performed using Illumina BovineSNP50 Beadchip. The number of phenotype data and genotype data were 107, and 294. respectively. Phenotype data were collected for four periods (0 week, 1 week, 4 week, 24 week) after having vaccinated (0 week no vaccinated period). A total of 36,257 SNPs was remained after quality control had been done by PLINK. The result of GWAS showed 6 SNP markers (BTB-01704243, BTB-01594395, ARS-BFGL-NGS-118070, ARS-BFGL-NGS-111365, BTA-65410-no-rs, Hapmap38331-BTA-61256) under BVDV and 4 SNP markers (ARS-BFGL-NGS-109861, Hapmap53701-rs29017064, ARS-BFGL-NGS-71055, BTA-11232-no-rs) under BRSV. And also, 10 candidate genes found through 10 SNP markers (TBX18, CEP162, PAFAH1B1, METTL16, BRCA1, RND2, POLK, ENSBTAG00000051724, ADAM18, NRG3).

• Food Science and Industry
• /
• v.52 no.3
• /
• pp.220-228
• /
• 2019

Rapid development of next-generation sequencing (NGS) technology is available to study microbes in genomic level. This NGS has been widely used in DNA/RNA sequencing for genome sequencing, metagenomics, and transcriptomics. The food microbiology area could be categorized into three groups. Food microbes including probiotics and food-borne pathogens are studied in genomic level using NGS for microbial genomics. While food fermentation or food spoilage are more complicated, their genomic study needs to be done with metagenomics using NGS for compositional analysis. Furthermore, because microbial response in food environments are also important to understand their roles in food fermentation or spoilage, pattern analysis of RNA expression in the specific food microbe is conducted using RNA-Seq. These microbial genomics, metagenomics, and transcriptomics for food fermentation and spoilage would extend our knowledge on effective utilization of fermenting bacteria for health promotion as well as efficient control of food-borne pathogens for food safety.

• Journal of Life Science
• /
• v.25 no.3
• /
• pp.349-356
• /
• 2015

Thanks to recent advances in next-generation sequencing (NGS) technology, diverse livestock species have been dissected at the genome-wide sequence level. As for cattle, there are currently four Korean indigenous breeds registered with the Domestic Animal Diversity Information System of the Food and Agricultural Organization of the United Nations: Hanwoo, Chikso, Heugu, and Jeju Heugu. These native genetic resources were recently whole-genome resequenced using various NGS technologies, providing enormous single nucleotide polymorphism information across the genomes. The NGS application further provided biological such that Korean native cattle are genetically distant from some cattle breeds of European origins. In addition, the NGS technology was successfully applied to detect structural variations, particularly copy number variations that were usually difficult to identify at the genome-wide level with reasonable accuracy. Despite the success, those recent studies also showed an inherent limitation in sequencing only a representative individual of each breed. To elucidate the biological implications of the sequenced data, further confirmatory studies should be followed by sequencing or validating the population of each breed. Because NGS sequencing prices have consistently dropped, various population genomic theories can now be applied to the sequencing data obtained from the population of each breed of interest. There are still few such population studies available for the Korean native cattle breeds, but this situation will soon be improved with the recent initiative for NGS sequencing of diverse native livestock resources, including the Korean native cattle breeds.