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.

당뇨병성 신경병증에서 근위부 비골신경전도 검사를 이용한 병태생리학적 접근

김동현,이강건,박종원,박태환,안병철,권오상 대한신경과학회 1998 대한신경과학회지 Vol.16 No.2

TINA 기반의 인터넷 멀티미디어 서비스 구조 설계

권태형,이상백,박동선,이경휴 한국정보전략학회 1999 추계공동학술대회 논문집 Vol.- No.01

본 논문에서는 TINA 기반의 인터넷 멀티미디어 서비스 구조를 설계하였다. 설계한 구조는 PSTN을 사용하여 인터넷에서 멀티미디어 서비스를 위한 Qos를 보장할 수 있도록 하였다. 본 논문에서 제시한 구조에서는 TINA 비즈니스 모델을 이용하여 사용자는 손쉽게 다양한 멀티미디어 서비스를 이용할 수 있도록 하고, 서비스 제공자는 서비스 제공이 손쉬우며 망 사업자 측면에서는 서비스 활성화에 따른 망 사용 증가로 인해 망 수요를 증가 시킬 수 있도록 하였다.

α-Amylase Inhibitor 생산균 Streptomyces sp. AI-118의 분리 및 동정

권태종,서동진 建國大學校 附設 産業技術硏究所 1992 논문집 Vol.17 No.-

a-amylase의 효소작용을 저해하는 물질을 생산하는 균주를 토양에서 분리, 동정하였으며 저해물질 생산의 최적 조건을 검토하였다. 본균을 방선균 종정법에 따라 결과 새로운 균주로 판명되어 Streptomyces sp. AI-118이라고 명명하였다. 본 균주는 탄소원으로 corn starch 3.0%, 질소원으로 soy bean meal 1.0%, 무기염으로 NaCI 0.05%, MnSO₄·4H₂O 0.0001%, CuSO₄·5H₂O 0.0001%를 사용한 배지에서 initial pH 6.0, 30℃ 그리고 배양 72시간일 때 최대의 저해물질을 생산하였다. A microorganism, strain AI-118, capable of producing a new a-amylase inhibitor in culture broth was isolated from soil and identified as Streptomyces sp. on the morphological, cultural and physiological characteristics. The preferable medium composition has been determined to be as follows:3.0% corn starch, 1.0% soy bean meal, 0.05% NaCl, 0.05% K₂HPO₄, 0.0001%MnSO₄· 4H₂O and 0.0001% CuSO₄·5H₂O(pH6.0). The inhibitor was maximally produced after 60-80hr cultivation in a jar fermentor at 30℃.

흰쥐에서 탄수화물 종류가 운동시 당 및 지질대사에 미치는 영향

권태동,전중기,민경선,김형렬,장응찬 대구대학교 기초과학연구소 1998 基礎科學硏究 Vol.15 No.2

The purpose of this study was to investigate the effects of glucose, sucrose, and glucose polymer(GP) ingestion on the carbohydrate and lipid metabolism during treadmill running in rats. Rats were randomly assigned to normal, control and carbohydrate groups. Carbohydrate group was divided into glucose, sucrose and GP ingested rats. The experiment was carried out after overnight fasting. Rats were administrated either normal saline(control) or carbohydrates solutions of formulated glucose(6%), sucrose(6%) and GP(6%) via polyethlene tube to stomach before treadmill run. Exercise was loaded by a treadmill run at the speed of 1 km/hour for 30, 60 and 120 minutes. The results of experiment were as follows: Plasma glucose levels were decreased in proportion to the exercise time in control, but increased at treadmill run 30 minutes and then gradually decreased with the lapse of the exercise time in carbohydrates compared with normal rats. It decreased in control, glucose, sucrose and GP compared with normal rats in decreasing order at treadmill run 120 minutes(% change of plasma glucose level of control, glucose, sucrose and GP compared with normal rats were 67, 74, 87 and 91 in plasma glucose level at treadmill run 120 min., respectively). Plasma lactate levels were increased by the exercise loading compared with normal in control and carbohydrates ingested rats. It increased in control, sucrose and GP in increasing order compared with normal rats, at treadmill run 120 minutes(% change of plasma lactate level of control, glucose, sucrose and GP compared with normal rats were 167, 185, 149 and 114 in plasma lactate level at treadmill run 120 min., respectively). Plasma FFA levels had tendency to increase by the exercise loading compared with normal in control and carbohydrates ingested rats. It showed increase in the sucrose, glucose, GP and control rats in Increasing order compared with normal rats at treadmill run 120 minutes(% change of plasma FFA level of control, glucose, sucrose and GP compared with normal rats were 151, 153, 166 and 152 in plasma FFA level at treadmill run 120 min., respectively). Plasma acetoacetate levels were higher in control compared with carbohydrates ingested rats at treadmill run 30, 60 and 120 minutes. Plasma beta-hydroxybutyrate levels increased by exercise compared with normal rats in control and carbohydrates ingested rats at treadmill run 30, 60, 120 minutes. Plasma insulin levels were decreased in proportion to the exercise time in control compared with normal rats, but in carbohydrates ingested rats increased at treadmill run 30 minutes and then gradually deceased with the lapse of the exercise time compared with normal. In carbohydrates ingested rats, plasma insulin levies were higher than control. Hematocrit did not show any difference between control and carbohydrates rats at treadmill run 30, 60 and 120 minutes. From these experimental results, it is suggested that the exhaustion of skeletal muscle glycogen, the hypoglycemia, the overproduction of lactate and dehydration is delayed in carbohydrates ingested rats. GP of the carbohydrates is considered as the most effective for these effects. Therefore, intake of carbohydrates before exercise, especially GP seems to increase performance in the prolonged moderate exercise.

디니트로톨루엔과 메타디니트로벤젠의 接觸還元에 對한 反應機構

權泰東 울산과학대학 1979 연구논문집 Vol.4 No.2

디니트로톨루엔과 메타디니트로벤젠의 접촉환원반응을 Hougen-Watson Model을 이용하여 해석해 보았다. 그 결과 18개 Model중 최적 Model을 찾아 내었다. Investigations were undertaken on the catalytic reduction of dinitrotoluene and m-dinitrobenzene. This paper undertakes to investigate the interpretation of mechanism of reduction of dinitrotoluene and m-dinitrobenzene by Hougen-Watson Model. The result was one proper mechanism is determined from eighteen models.

Methanol 자화성 효모에 의한 균체 단백질 생산

권태종,이동희,정호권,최태부 건국대학교 1992 學術誌 Vol.36 No.2

SCP producing yeast JAM -3032 that has high productivity potential with methanol as carbon and energy source was isolated from soil, and conditions for SCP production, nutritional values, and alcohol oxidase of the microorganism were investigated. Isolated strain JAM-3032 was identified as Pichina on the morphological, cultural, physiological and biochemical characteristics. The production of cell mass reached at maximal level after 54 hrs cultivation at 28℃, pH 6.0 in the medium containing methanol 3.0%, yeast extract 0.8%, K2HPO4 0.1%, KH2PO4 0.1%. MgSO4ㆍ7H2O 0.05%, alanine 0.01%, nicotinic acid 0.04%, and biotin 0.04%. Dry cells of Pichia sp. JAM -3032 was composed of proteins 53.3%, carbohydrates 31. 5%, nucleic acids 5.6%, lipids 2.9%, ash 6.4% and amino acid composition of the proteins was satisfied in FAO reference. Biosynthesis of the alcohol oxidase of the strain JAM -3032 was induced by methanol. The enzyme was purified by treatment of ammonium sulfate fractionation, DEAE-Sephadex A-50 ion exchange chromatography and Sepharose 6B gel nitration. The purified enzyme was homogeneous on SDS-PAGE, and molecular weight was estimated to be about 520,000 D that was consisted of 8 subunits containing FAD as coenzyme. The optimal pH and temperature for the enzyme reaction was 7.5 and 37℃, respectively. Activation energy was 17.1Kcal/mol and half inactivating temperature was 40℃. The enzyme activity was inhibited by Ag+, Cu2+ and Hg2+ ions remarkably. The enzyme acted on methanol specifically, and its Km value was 0.89 mM.

단백뇨를 보이는 사구체 질환 및 당뇨병성 신병증에서의 Lp(a)

권태환,김준홍,조성,김석재,김용림,조동규,백미영 경북대학교 병원 1998 경북대학교병원의학연구소논문집 Vol.2 No.1

Background: Recently there has been evidences that serum Lp(a), an independent risk factor to atherosclerotic cardiovascular diseases, were increased in proteinuric disorders such as nephrotic syndrome and diabetic nephropathy. Methods: We intended to search of altered concentrations of Lp(a) in proteinuric disorder measuring serum Lp(a) concentrations with ELISA in 44 glomerulonephritic patients(25 nephrotic syndrome(NS), 19 non-nephrotic range proteinuric glomerulonephritis(GN), 25 diabetic nephropathy patients(DN), and 31 healthy controls(HC). Also, we compared Lp(a) concentration between glomerulonephritis patients and diabetic nephropathy patients with proteinuria of similar degree. Results: 1) There were significantly increased levels of total choesterol, triglyceride, and LDL-cholesterol in Ns compared to GN, DN, HC. 2) There were significantly increased concentrations of serum Lp(a) in NS compared to HC, but no signiicant difference in serum Lp(a) among NS, GN, and DN. 3) There was no significant difference in serum Lp(a) concentrations between NS & DN with 24 hour urine protein greater than 3.0g. 4) There was no significant difference in serum Lp(a) concentration between GN with 24 hour urine protein greater than 0.5g and less than 1.5g and DN with proteinuria of simial degree. 5) In glomerulonephritis patients, there was negative correlation between serum Lp(a) concentration and serum albumin level but correlation with 24 hour urinary protein, total cholesterol, Ldl-cholesterol, and HDL-cholesterol was not shown. In diabetic nephropathy, there was no significant correlation among serum Lp(a) concentration and all parameters including serum albumin, 24 hour urinary protein, and other lipid profiles. Conclusion: The present study confirmed that patients with nephrotic syndrome of diverse etiologies have makedly increased plasma level of Lp(a), in conjunction with other lipid abnormalities. However, this study shows no difference in Lp(a) concentrations between diabetic nephropathy and glomerulonephritis with similar degree of proteinuria.

알칼리수의 3 차원 초분자 구조에 관한 컴퓨터 분자 모델링

권태종,정호권,강상모,이동희,정선호 건국대학교 산업기술연구원 1997 건국기술연구논문지 Vol.22 No.-

The supramolecular structures of an alkaline or mineral water molecule were simulated and their various structural and dynamical properties were studied in comparison with those of the pure water molecules. Molecular modeling was performed with Quanta molecular interface program under the CHARm forcefields. Molecular mechanic calculation and molecular dynamic calculation were performed for pure and alkaline supramolecular water structures. The change of the number of hydrogen bondings, radius of Gyration and total dipole moment of the supramolecular structures for pure and alkaline water molecules were investigated as a function of temperature. Alkaline or mineral water were shown to be more energetically stable, more compact and more capable in formation of hydrogen bonds in their supramolecular structures.

일부 종합병원 간호사들의 요통 유병상태에 관한 조사연구

권순태,이동배,이태용 충남대학교 의과대학 지역사회의학연구소 1991 충남의대잡지 Vol.18 No.2

A questionaire survey was conducted on 482 hospital nurses in Taejeon City to investigate the prevalence & epidemiolgical characteristics of work related LBP during past six mouths. The results obtained were as follows. 1. Overall 6 months prevalence rate of LBP was 49.5% & mean duration of LBP were 10.8 days. 2. 6 months prevalence rate of LBP was the highest among nurses of care unit with 61.4% & mean duration of LBP were significantly longer among nurses of care unit with 17.7 days than other department workers. 3. 6 months prevalence rate of LBP was significantly higher among groups lifting frequency/day more than 20 with 62.9% than below 20 group with 46.1% (P<0.01). 4. Back injury rate was 27.4% with lumbar sprain with 19.5%, contusion with 7.5%. 5. Back injury rate was significantly higher among care-unit workers with 32.4% (P<0.05) than other department workers. 6. 10.8% of workers with LBP experienced absenteeism due to LBP. Among the injured, only 39.6% ran been treated.