NGS_SNPAnalyzer: a desktop software supporting genome projects by identifying and visualizing sequence variations from next-generation sequencing data

Dong‑Jun Lee,Taesoo Kwon,Chang‑Kug Kim,Young‑Joo Seol,Dong‑Suk Park,Tae‑Ho Lee,Byung‑Ohg Ahn 한국유전학회 2020 Genes & Genomics Vol.42 No.11

Background Sequence variations such as single nucleotide polymorphisms are markers for genetic diseases and breeding. Therefore, identifying sequence variations is one of the main objectives of several genome projects. Although most genomeproject consortiums provide standard operation procedures for sequence variation detection methods, there may be differencesin the results because of human selection or error. Objective To standardize the procedure for sequence variation detection and help researchers who are not formally trainedin bioinformatics, we developed the NGS_SNPAnalyzer, a desktop software and fully automated graphical pipeline. Methods The NGS_SNPAnalyzer is implemented using JavaFX (version 1.8); therefore, it is not limited to any operatingsystem (OS). The tools employed in the NGS_SNPAnalyzer were compiled on Microsoft Windows (version 7, 10) andUbuntu Linux (version 16.04, 17.0.4). Results The NGS_SNPAnalyzer not only includes the functionalities for variant calling and annotation but also providesquality control, mapping, and filtering details to support all procedures from next-generation sequencing (NGS) data to variantvisualization. It can be executed using pre-set pipelines and options and customized via user-specified options. Additionally,the NGS_SNPAnalyzer provides a user-friendly graphical interface and can be installed on any OS that supports JAVA. Conclusions Although there are several pipelines and visualization tools available for NGS data analysis, we developedthe NGS_SNPAnalyzer to provide the user with an easy-to-use interface. The benchmark test results indicate that theNGS_SNPAnayzer achieves better performance than other open source tools.

영동포도의 유통실태 및 경재력 향상에 관한 연구

권원달,최동주,정진영 충북대학교 농업과학기술연구소 2000 農業科學硏究 Vol.17 No.-

Yongdong region is semi-mountainous area. The sea levels of Yongdong-gun is around 100∼300m, the annual average temperature is 11.5℃ and the annual average difference of temperature between day and night is 10∼15℃. Thus the weather conditions of Yongdong region was suitable for grape production especially in sweetening and coloring of grape during ripening season. To promote commodity attributes of Yongdong Grape it is needed to introduce grading, standardization, improving packing and using a trade-mark. To open and extend new market it is necessary activating shipping organization, selecting practicalize market supplying marketing information, advertising, and publicizing. There were three grape processing companies in Yongdong-Gun. They were mostly small sized and purchased and used only 877 M/T (2.9% of total production) of grapes as a raw materials. These grape processing companies produced very low added value because they sold there product as OEM, or at consumer market. Present grading and packing system which is managed by individual producer base is needed to introduce cooperative inspection system which units of grape shipping organization or regional cooperatives take part in inspection. Also introducing cooperative recording and accounting system would maximize internal economic effects of marketing. Future scope and function of cooperative grape farm organization of Youngdong-Gun would develop from partial cooperative organization which produce and pack grape by individual base but inspect, ship and trade by cooperative system to whole cooperative organization of which scope and function is expended to common brand of grape and Yongdong-gun level organization. Establishing information and publication's post in Yongdong-Gun building, constructing grape theme park and opening grape festival which is needed to attract tourist are needed to encourage and promote advertisement and publicity of Yongdong Grape.

Navier-Stokes 방법을 이용한 Blowing이 무딘물체 주위의 표면 열전달에 미치는 효과 연구

권창오,송동주 嶺南大學校 工業技術硏究所 1998 工業技術硏究所論文集 Vol.26 No.1

A finite-difference method based on characteristic upwind flux difference splitting Navier-Stokes method has been studied by using the blowing effect on the wall heat transfer rate over blunt-bodies. As the wall blowing rates increased, the wall heat transfer rate and the temperature gradient decreased compared with those of no blowing case. The heat transfer rate at Mach No. 20 was almost twice higher than that of Mach No. 15 at 60㎞ altitude. The surface blowing can be an effective mechanism to reduce the surface heat transfer rate at hypersonic flight condition.

3차원 금형절삭에 있어서 上下方向 切削特性 硏究

권영균,이동주 충남대학교 산업기술연구소 2000 산업기술연구논문집 Vol.15 No.2

In our study, the experiment tried to find the optimum cutting conditions and method by observing the cutting force working at ball end-mill varying axial depth and radial depth for upward cutting and downward cutting along the decline. As a result of the experiment, the cutting was more unstable in downward cutting than in upward cutting and also in the case of axial depth than in radial depth, which resulted from the fact that the cases of downward cutting and of radial depth had a relatively wider contact surface than that of upward cutting and of axial depth and approached the edge at extreme point of a tool more closely rather than a side blade, and the cutting force had a tendency to be reduced as the inclined angle increased.

외과계 감염증에 대한 Sulperazon(Sulbactam/cefoperazone) 및 Cefoperazone의 임상효과 비교연구

박규주,노동영,김상준,권오중,정중기,홍인규 대한화학요법학회 1990 대한화학요법학회지 Vol.8 No.2

Despite recent advances in development of antibiotics and antiseptic techniques, infection still remains to be one of the major problems in the surgical field. Due to development of bacterial resistance to commonly used antibiotics, there is always a need to develop a new antimicrobial agent which would overcome such resistance. Sulperazon (Sulbactam/Cefoperazone) is a combination drug of potent β-lactamase inhigitor, sulbactam, and cefoperazone which has broad antibacterial spectrum, which was developed to combat against β-lactamase producing microorganisms. In an effort to evaluate the efficacy and safety of sulperazone, we have randomly divided 40 patients (12 with perforated appendicitis, 10 with peritionitis, 6 with GB empyema, 6 with periproctal abscess, 3 with wound infection, 1 liver abscess, 1 pancreatic abscess, and 1 acute cholangitis) into 2 groups (20 patients in each group). One group received daily dose of 2 to 3 grams of sulperazon and the other group received daily dose of 2 to 3 grams of cefoperazone. Following results were obtained : 1. Clinical effect of sulperazon was cure in 16 patients (80%), improvement in 3 patients (15%), compaired to cure in 14 patients (70%), improvement in 4 patients (20%) for the cefoperazone group. 2. Using disc diffusion method, sulperazon was sensitive to all of the isolated microorganisms except β-hemolytic streptococci, which was moderately sensitive. Cefoperazone was sensitive to only E. coli, Pseudomonas aeruginosa and Serratia. 3. Microbiological effect of sulperazon was eradication of offending microorganisms in 16 patients (80%), compared to 14 patients (70%) in Cefoperazone group. 4. Overall clinical efficacy of sulperazon was 95%, compared to 80% for cefoperazone. 5. Adverse effects due to sulperazon was nausea and diarrhea which occurred in 1 patient respectively. 2 patients receiving cefoperazone experienced diarrhea. It can be concluded that sulperazon is a safe and effective antibiotic agent which can be used in surgical infection patients.

수영만 해역의 오염물질 거동에 대한 小考

이은주,한동진,권정곤 부산대학교 환경문제연구소 1994 環境硏究報 Vol.12 No.-

This study aims to make it clear the mechanism on the behavior of pollutant in Suyeong Bay using the Alternating Direction Implicit method which was used for forecasting coastal water quality with good capability in stability and calculative velocity. And the flow fields for diffusion calculation were consisted of tidal current, tidal residual flow and constant flow(tidal residual flow+wind-induced flow) which are depth-averaged in total time, respectively.

Paclitaxel 및 Apo-2L/TRAIL이 자궁경부암 세포주 아포토시스에 미치는 영향

김주영,남계현,김태희,이권해,이해혁,배동한 순천향의학연구소 2003 Journal of Soonchunhyang Medical Science Vol.9 No.2

Objective: TRAIL(also called Apo-2L) is a member of the tumor necrosis factor(TNF) family of cytokines which induces apoptosis cell death in a variety of tumor cell lines. It mediates its apoptotic effects through one of two receptors, DR4 and DR5, which are members of the TNF receptor family, and whose cytoplasmic regions contain death domains. TNF and Fas ligand induces apoptosis in tumor cells; however, their severe toxicity toward normal tissues hampers their application to cancer therapy. We examed if paclitaxed and/or Apo-2LTRAIL induces apoptosis of cervical cancer HeLa, SiHa, ME-180, and CaSki cells. Mehods : We have demonstrated that paclitaxel and Apo-2L/TRAIL induces apoptosis of cervical cancer HeLa, SiHa, CaSki and ME-180 cell lines in a dose-dependent manner. HeLa, SiHa, ME-180 and CaSki were obtained from American Type Culture Colection. Recombinant Human TRAIL(Chmicon). DR4 and DR5 were purchased from Santa Cruz. Paclitaxel, MTT assay Kit, Acridine orange and Ethium bormide were purchased from Sigma. HeLa and SiHa were grown in DMEM. ME-180 and CaSki were grown in RPMI. Tripan blue stain and MTT assay were done for cytotoxicity. Annexin V-FITC and PI(propidium iodide) flowcytometry for apoptosis assay. DR4 and DR% were expressed by Western Blot. Fluorescent Microscopy used Acridine orange(AO) and Ethium bromide(EB). Results : Importantly, concurrent treatment of cervical cancer cells with paclitaxed and Apo-2L/TRAIL induces significantly more apoptosis than Apo-2L/TRAIL alone. Conclusion : We need further studies which reveals possible therapeutic potential in the women with cervical cancer by suing Apo-2L/TRAIL.

Polyester 신합섬 직물의 농색염색 및 대전방지가공에 관한 연구 (Ⅰ)

김동권,이주형,이난형,김삼수,조환 영남대학교 지역발전연구소 1996 새마을지역개발연구 Vol.18 No.-

The Dyeing processing, which can be a low-cost and easily application to production field was investigated by using some bathochromic agent and dyestuffs. The Δ L values and dye up-takes of threated several fabrics were investigated according to the dye concentration and pH of dyebath. The results were as follows : 1. The selection of bathochromic agent acts as important factor for improvment of bathochromic property of fabrics. 2. The pH of dyebath has a little effect on bathochromic effect. 3. In case of one bath treatment, the bathochromic agent has little effect on the improving bathochromic property of treated fabric. 4. The efficiency order of bathochromic effect is DTY + fila.> CVY > DTY and fabric structure is also effect on the bathochromic property of the polyester fabric.

항공 예약을 위한 실시간 음성 인식기 구현

이주헌,함동훈,권영헌,이건상 한양대학교 이학기술연구소 2002 이학기술연구지 Vol.5 No.-

현재 항공기 예약 시스템을 사용하기 위해서 사용자는 전화, 인터넷 들을 이용하고 있다. 이러한 시스템은 상호 인터페이상의 제약에 따른 불편함이 있다. 본 논문은 음성 인식 기술을 바탕으로 보다 쉽고, 편리하게 항공기 예약 시스템을 사용할수 잇도록 실시간 인식기를 구현하였다. 음성 DB(database)는 인터넷상 예약 모델 시나리오에 기초하여 70여개의 단어에 대하여 5명의 화자에 대하여 20번씩 발음한 것을 이용하였다. code-book은 tri-phone을 기반으로 작성 하였으며,인식 속도의 향상을 위하여 인식 어휘에 따라 4종류로 code-book을 분리하여 5명의 훈련화자에 대해서는 선택 출발 도착지별 99.41%, 예매 인원수별 90.13%, 월별 74.17%, 일별 86.21%의 인식률을 얻었으며,테스트 화자(2명의 화자가 70여개의 단어에 대하여 5번씩 발음)에 대해서는 선택 출발 도착지별 97.47%, 예매 인원수별 90.00%, 월별 48.33%, 일별 75.48%의 인식률을 얻었다. Usually a user makes a reservation of airplane, through phone or internet etc. This brings some inconvenience such as restriction of mutual interface. This paper studies a realtime speech recognizer by which user conveniently makes use of aircraft It reservation system. We construct a speech database, which is based on the scenario of the reservation model in the Internet service, by recording 70 words pronounced by 5 speakers 20 times. Also for improving the recognition speed, we compose the code-book with four parts(departure and arrival, head count, month, and day). Then the recognition rates of 5 trained speakers are99.41% for departure and arrival section, 90.13% for the head count in advance purchase,74.17% for a month, and 86.21% for a day, and ones of 2 test speakers are 97.47%, 90.00%,48.33%, and 75.48%, respectively.

일본잎갈나무 낙엽의 추출성분 및 항산화활성

사전령,권동주,김진규,황병호,배영수 江原大學校 森林科學硏究所 2005 Journal of Forest Science Vol.21 No.-

일본잎갈나무 낙엽 (8.5kg)을 채취하여 9.5% EtOH 용액으로 추출하고 농축된 추출용액은 분획깔때기로 헥산, 메틸렌클로라이드, 에틸아세테이트 및 수용성으로 순차 추출하여 동결건조하였다. 에틸아세테이트용성과 수용성 분획에 대하여 칼럼크로마트크래피를 실시하였고, 충진물질로는 Sephadex LH-20을, 용리용매로는 메탄올 수용액 및 에탈올-핵산 혼합용액을 사용하였다. 단리된 화합물들은 TLC로 확인한 후 NMR 스펙트럼을 사용하여 정확한 구조규명을 하였고 FAB-MS와 EI-MS 스펙트럼으로 분자량을 측정하였다. 일본잎갈나무 낙엽으로부터 5개의 화합물을 단리하였으며, 각 분획물과 단리된 화합물들은 DPPH 라디칼 소거법을 이용하여 항산화 시험을 실시하였다. Fallen neeldes (8.5kg) of Larix kaempferi were separately collected. extracted with 95% EtOH. EtOH extract was evaporated under reduced pressure, concentrated then successively fractionated with a series of hexane. methylene chloride, ethylaectate and water on a separatory funnel. Then, each fraction was freeze dried. A portion of ethylacetate and water soluble powder were packed on a column chromatography (Sephadex LH-20) eluting with aqueous MeOH and EtOH-hexane mixture. Spectrometric analyses such as NMR and FAB-MS including TLC were performed to characterize the structures of isolated compounds.