• Journal of Microbiology and Biotechnology
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• 제26권1호
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• pp.207-212
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• 2016

PacBio's long-read sequencing technologies can be successfully used for a complete bacterial genome assembly using recently developed non-hybrid assemblers in the absence of second-generation, high-quality short reads. However, standardized procedures that take into account multiple pre-existing second-generation sequencing platforms are scarce. In addition to Illumina HiSeq and Ion Torrent PGM-based genome sequencing results derived from previous studies, we generated further sequencing data, including from the PacBio RS II platform, and applied various bioinformatics tools to obtain complete genome assemblies for five bacterial strains. Our approach revealed that the hierarchical genome assembly process (HGAP) non-hybrid assembler resulted in nearly complete assemblies at a moderate coverage of ~75x, but that different versions produced non-compatible results requiring post processing. The other two platforms further improved the PacBio assembly through scaffolding and a final error correction.

• 한국도서관정보학회지
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• 제26권
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• pp.261-290
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• 1997

98 wise sayings on the nature of book are collected from various books and analyzed in their meanings. The results of analyzing them are as follows: A book is a good friend, teacher, doctor, and guide of life. A book is an implement of enhancing man s culture and a vehicle of civilization. A book makes man find his own self and shows his way of life. A book has its own life, develops it, and doesn't lose its life, but its destination depends on its reader. Great books make man know, dominate, civilize the world. Good books are not easy to come in contact with, but immortal and life-long as a good friend. Bad books are not difficult to come in contact with, but poisonous and dull. You can judge a man by the book he reads. A book to be of help is to make man think. Great books make man begin his new life. Nationalities occupations, and periods of activity of the authors who said wise sayings are investigated and analyzed. First, the nationalities of the authors are such advanced countries with high culture as England(41%), France(21%), America(19%), Germany(5%) and Rome(5%). Secondary, their occupations are as follows : a man of letters(62%), philosopher(13%), politician(5%), and churchman(4%), and especially poet forms 32% of men of letters. Thirdly, their activity periods are mainly 19C-20C and the period form 38% of the whole.

• 대한전자공학회논문지SD
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• 제44권1호
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• pp.45-50
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• 2007

본 논문에서는 상변환 메모리 (phase-change random access memory: PRAM)의 저전력 선택적 데이터 쓰기(selective data write: SDW) 기법을 제안하였다. PRAM은 쓰기 동작 과정에서 큰 전류를 오랜 시간동안 소모하기 때문에 큰 쓰기 전력을 소모한다. 이 쓰기 전력을 줄이기 위하여, SDW 기법은 쓰기 동작 과정에서 PRAM 셀에 데이터를 쓰기 전에 우선 저장될 셀의 데이터를 읽어온다. 셀의 기존 데이터와 새롭게 저장할 데이터를 비교하여, 입력된 데이터와 저장된 데이터가 다른 경우에만 PRAM 셀에 데이터 쓰기를 수행한다. 제안된 쓰기 기법을 사용하여 전력 소모를 반 이상으로 줄일 수 있다. 1Kbits ($128{\times}8bits$) PRAM 테스트 칩을 $0.5{\mu}m$ GST 셀과 $0.8{\mu}m$ CMOS 공정을 사용하여 구현하였다.

• 한국CDE학회논문집
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• 제8권2호
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• pp.65-74
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• 2003

For virtual reality, virtual manufacturing system, or simulation based design, we need to visualize very large and complex 3D models which are comprising of very large number of polygons. To overcome the limited hardware performance and to attain smooth realtime visualization, there have been many researches about algorithms which reduce the number of polygons to be processed by graphics hardware. One of these algorithms, occlusion culling is a method of rejecting the objects which are not visible because they are occluded by other objects, and then passing only the visible objects to graphics hardware. Existing occlusion culling algorithms have some shortcomings such as the required long preprocessing time, the limitation of occluder shape, or the need for special hardware implementation. In this study, an efficient occlusion culling algorithm is proposed. The proposed algorithm reads and analyzes Z-buffer of graphics hardware using Microsoft DirectX, and then determines each object's visibility. This proposed algorithm can speed up visualization by reading Z-buffer using DirectX which can access hardware directly compared to OpenGL, by reading only the region to which each object is projected instead of reading the whole Z-Buffer, and the proposed algorithm can perform more exact visibility test by using simplified model instead of using bounding box. For evaluation, the proposed algorithm was applied to very large polygonal models. And smooth realtime visualization was attained.

• Asian-Australasian Journal of Animal Sciences
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• 제32권7호
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• pp.1044-1051
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• 2019

Objective: Recent studies have implied that gene expression has high tissue-specificity, and therefore it is essential to investigate gene expression in a variety of tissues when performing the transcriptomic analysis. In addition, the gradual increase of long non-coding RNA (lncRNA) annotation database has increased the importance and proportion of mapped reads accordingly. Methods: We employed simple statistical models to detect the sexually biased/dimorphic genes and their conjugate lncRNAs in 40 RNA-seq samples across two factors: sex and tissue. We employed two quantification pipeline: mRNA annotation only and mRNA+lncRNA annotation. Results: As a result, the tissue-specific sexually dimorphic genes are affected by the addition of lncRNA annotation at a non-negligible level. In addition, many lncRNAs are expressed in a more tissue-specific fashion and with greater variation between tissues compared to protein-coding genes. Due to the genic region lncRNAs, the differentially expressed gene list changes, which results in certain sexually biased genes to become ambiguous across the tissues. Conclusion: In a past study, it has been reported that tissue-specific patterns can be seen throughout the differentially expressed genes between sexes in cattle. Using the same dataset, this study used a more recent reference, and the addition of conjugate lncRNA information, which revealed alterations of differentially expressed gene lists that result in an apparent distinction in the downstream analysis and interpretation. We firmly believe such misquantification of genic lncRNAs can be vital in both future and past studies.

• 생명과학회지
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• 제29권1호
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• pp.1-8
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• 2019

한우(한국 재래 소)에서 반수체형 페이징을 위한 고밀도 시퀀싱을 이용한 비교 분석 논문은 많지가 않다. 이런 고밀도 시퀀싱 플랫폼 중에서, 일루미나에서 서비스 하는 Truseq Synthetic Long-Read Haplotyping 시퀀싱 플랫폼(TSLRH)과 10X Genomics에서 서비스하는 The Chromium Genome 시퀀싱 플랫폼을 특별히 비교 분석하는 논문은 없다. 우리는 한우 연구소의 한우 종모우(아이디: TN1505D2184 or 27214)의 정액에서 DNA를 추출하였으며, 이 DNA로부터 각각의 시퀀싱 플랫폼을 이용하여 시퀀싱 데이터를 생산하였다. 그 후, 우리는 각각의 시퀀싱 플랫폼에 맞는 분석 방법을 이용하여 단일염기서열변이들은 찾아냈다. 그 결과, TSLRH과 10XG의 전체 리드 수는 각각 355,208,304, 1,632,772,004, 맵핑 리드의 개수는 351,992,768(99.09%), 1,526,641,824(93.50%), Q30(%)은 89.04%, 88.60%, 평균 밀도는 13.04X, 74.3X, 가장 긴 페이즈 블락은 1,982,706bp, 1,480,081 bp, N50 페이즈 블락은 57,637 bp, 114,394 bp, 전체 단일염기서열변이는 4,534,989, 8,496,813, 전체 페이징 비율은 72.29%, 87.67%였다. 더욱이, 우리는 각각의 시퀀싱 플랫폼을 비교해서 각각의 시퀀싱 플랫폼의 고유한 단일염기서열변이와 두 시퀀싱 플랫폼에서 공통적으로 존재하는 단일염기서열변이를 각 염색체 별로 확인하였으며, 단일염기서열변이의 개수는 염색체 길이에 정비례한다는 결과를 확인하였다. 결론적으로, 본 연구에서 추천하는 바는 연구비가 충분하지 않을 시에는 TSLRH 보다 10XG을 사용하는 것을 추천한다. 왜냐하면 전체 리드 및 단일염기서열변이 개수, N50 페이즈 블락, 가장 긴 페이즈 블락, 페이즈 비율 그리고 평균 밀도 등이 TSLRH 보다 10XG가 더 높거나 좋기 때문이다.

• Asian-Australasian Journal of Animal Sciences
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• 제30권9호
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• pp.1215-1224
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• 2017

Objective: To assess the differences in ovarian transcriptomes in Shan Ma ducks between their peak and late stages of egg production, and to obtain new transcriptomic data of these egg-producing ducks. Methods: The Illumina HiSeq 2000 system was used for high throughput sequencing of ovarian transcriptomes from Shan Ma ducks at their peak or late stages of egg production. Results: Greater than 93% of the sequencing data had a base quality score (Q score) that was not less than 20 (Q20). From ducks at their peak stage of egg production, 42,782,676 reads were obtained, with 4,307,499,083 bp sequenced. From ducks at their late stage of egg production, 45,316,166 reads were obtained, with 4,562,063,363 bp sequenced. A comparison of the two datasets identified 2,002 differentially expressed genes, with 790 upregulated and 1,212 downregulated. Further analysis showed that 1,645 of the 2,002 differentially expressed genes were annotated in the non-redundant (NR) database, with 646 upregulated and 999 downregulated. Among the differentially expressed genes with annotations in the NR database, 696 genes were functionally annotated in the clusters of orthologous groups of proteins database, involving 25 functional categories. One thousand two hundred four of the differentially expressed genes with annotations in the NR database were functionally annotated in the gene ontology (GO) database, and could be divided into three domains and 56 categories. The three domains were cellular component, molecular function, and biological process. Among the genes identified in the GO database, 451 are involved in development and reproduction. Analysis of the differentially expressed genes with annotations in the NR database against the Kyoto encyclopedia of genes and genomes database revealed that 446 of the genes could be assigned to 175 metabolic pathways, of which the peroxisome proliferator-activated receptor signaling pathway, insulin signaling pathway, fructose and mannose metabolic pathways, gonadotropin releasing hormone signaling pathway and transforming growth factor beta signaling pathway were significantly enriched. Conclusion: The differences in ovarian transcriptomes in Shan Ma ducks between their peak and late stages of egg production were elucidated, which greatly enriched the ovarian transcriptomic information of egg-producing ducks.

• 한국군사과학기술학회지
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• 제27권4호
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• pp.507-515
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• 2024

Microbial forensics is a scientific discipline for analyzing evidence related to biological crimes by identifying the origin of microorganisms. Multiple locus variable number tandem repeat analysis(MLVA) is one of the microbiological analysis methods used to specify subtypes within a species based on the number of tandem repeat in the genome, and advances in next generation sequencing(NGS) technology have enabled in silico anlysis of full-length whole genome sequences. In this paper, we analyzed unknown samples provided by Robert Koch Institute(RKI) through The United Nations Secretary-General's Mechanism(UNSGM)'s external quality assessment exercise(EQAE) project, which we officially participated in 2023. We confirmed that the 3 unknown samples were B. anthracis through nucleic acid isolation and genetic sequence analysis studies. MLVA results on 32 loci of B. anthracis were analysed by using genome sequences obtained from NGS(NextSeq and MinION) and Sanger sequencing. The MLVA typing using short-reads based NGS platform(NextSeq) showed a high probability of causing assembly error when a size of the tandem repeats was grater than 200 bp, while long-reads based NGS platform(MinION) showed higher accuracy than NextSeq, although insertion and deletion was observed. We also showed hybrid assembly can correct most indel error caused by MinION. Based on the MLVA results, genetic identification was performed compared to the 2,975 published MLVA databases of B. anthracis, and MLVA results of 10 strains were identical with 3 unkonwn samples. As a result of whole genome alignment of the 10 strains and 3 unknown samples, all samples were identified as B. anthracis strain A4564 which is associated with injectional anthrax isolates in heroin users.

• 한국토양비료학회지
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• 제45권6호
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• pp.1100-1107
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• 2012

화학비료의 장기 시용이 벼 내생 세균 군집에 미치는 영향을 조사하기 위해서 국립농업과학원의 장기 비료 연용 포장에서 재배한 벼 뿌리의 내생균의 군집을 파이로시퀀싱 기법으로 분석하였다. 3요소구 (APK)와 무비구 (NF) 시료에서 직접 DNA를 추출하여 세균에 특이적인 barcode PCR을 수행한 후 454 파이로시퀀싱을 하였다. 두 시료 (3요소구, 무비구)에서 1,900개의 염기서열을 얻었으며, 각각 177개와 72개의 OTU로 분류하였다. 두 시료는 22개의 OTU를 공유하였으며, 이들 OTU는 두 시료에서 모두 우점하였다. 특히 Pseudomonas속에 속하는 OTU의 비율이 매우 높았다. 문 (phylum) 수준에서 우점하는 내생균은 두 시료 모두 Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Actinobacteria 등 이었다. 처리구별로 계산한 다양성 지수는 3요소구 시료에서 더 높았다. 본 연구를 통해 장기간 비료 시용은 식물체내 존재하는 내생균 군집 구조에 영향을 주며, 벼 뿌리의 내생 세균의 군집 다양성을 증가시키는 것을 알 수 있었다.

• 인지과학
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• 제3권2호
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• pp.225-248
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• 1992

본 논문에서는 의미 네트워크에 기반을 둔 지식베이스를 이용하여 단어 의미의 모호성을 해소하는 방법들을 소개 한다. 기본이 되는 방법은 입력문자의 의미해석이 진행됨에 따라 수집되는 지식베이스내의 경로(path)들을 추적하여 이용하는 것이다. 이러한 경로들을 의미경로(semantic path)라고 부른다. 파싱과정에서 한 단어가 입력되면 이단어가 가질수 있는 의미 중에서 어느 의미 경로에도 이용되지 않은 것들이 제거된다. 각 제거는 의미 경로들을 통하여 전파되어 이미 입력된 다른 단어들의 의미의 제거를 유발한다. 이 박업은 더이상 제거되는 의미가 없을때 까지 반복 진행된느데 이를 recursive word sense removal 작업이라 부른다. 추상적인 개념의 구체화(conctetion) 작업도 단어 의미 모호성해소의 중요한 방법인데, 본 논문에서는 이를 경로조절작업(path adjustment operation)이라고 불리는 방법을 이용하여 확장시키는 방법을 소개한다. 의미사이의 연과성(semantic association)이나 구문분석으로부터의 정보를 위의 방법들과 관련지어 이용하는 방법도 살펴본다.