• Title/Summary/Keyword: dot plot

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NBLAST: a graphical user interface-based two-way BLAST software with a dot plot viewer

  • Choi, Beom-Soon;Choi, Seon Kang;Kim, Nam-Soo;Choi, Ik-Young
    • Genomics & Informatics
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    • v.20 no.3
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    • pp.36.1-36.6
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    • 2022
  • BLAST, a basic bioinformatics tool for searching local sequence similarity, has been one of the most widely used bioinformatics programs since its introduction in 1990. Users generally use the web-based NCBI-BLAST program for BLAST analysis. However, users with large sequence data are often faced with a problem of upload size limitation while using the web-based BLAST program. This proves inconvenient as scientists often want to run BLAST on their own data, such as transcriptome or whole genome sequences. To overcome this issue, we developed NBLAST, a graphical user interface-based BLAST program that employs a two-way system, allowing the use of input sequences either as "query" or "target" in the BLAST analysis. NBLAST is also equipped with a dot plot viewer, thus allowing researchers to create custom database for BLAST and run a dot plot similarity analysis within a single program. It is available to access to the NBLAST with http://nbitglobal.com/nblast.

The Study of the Accuracy of Acereage (측정법(測定法)에 따른 면적측정(面積測定)의 정도(精度))

  • Kim, Kap D.
    • Journal of Korean Society of Forest Science
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    • v.6 no.1
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    • pp.24-26
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    • 1967
  • 1. The purpose of this experiment was to compose the precision of dot grid method and transects method with that of pianimeter method in area measurement. 2. The following conclusions were obtained through study on precision of area measurement of 20 plots. 3. The percentage error of each method was none significant in comparision with planimeter method. 4. The dot grid method gave 0.2% of overestimated value and the transects method 0.67% of underestimated value. 5. Accordingly, the dot grid method gave the better result than the transects method. 6. The transects method had small errors at the plots larger than 30ha. while it had big errors at plots smaller than 30ha. Therefore, it can be said that the transects method is suitable for area measurement of plots larger than 30 hectares.

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Molecular Theory of Plastic Deformation (Ⅲ)$^*$

  • Kim, Jae-Hyun;Ree, Tai-Kyue;Kim, Chang-Hong
    • Bulletin of the Korean Chemical Society
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    • v.2 no.3
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    • pp.96-104
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    • 1981
  • (1) The flow data of f (stress) and ${\dot{s}$ (strain rate) for Fe and Ti alloys were plotted in the form of f vs. -ln ${\dot{s}$ by using the literature values. (2) The plot showed two distinct patterns A and B; Pattern A is a straight line with a negative slope, and Pattern B is a curve of concave upward. (3) According to Kim and Ree's generalized theory of plastic deformation, pattern A & B belong to Case 1 and 2, respectively; in Case 1, only one kind of flow units acts in the deformation, and in Case 2, two kinds flow units act, and stress is expressed by $f={X_1f_1}+{X_2f_2}$where $f_1\;and\;f_2$ are the stresses acting on the flow units of kind 1 and 2, respectively, and $X_1,\;X_2$ are the fractions of the surface area occupied by the two kinds of flow units; $f_j=(1/{\alpha}_j) sinh^{-1}\;{\beta}_j{{\dot{s}}\;(j=1\;or\;2)$, where $1/{\alpha}_j\;and\;{\beta}_j$ are proportional to the shear modulus and relaxation time, respectively. (4) We found that grain-boundary flow units only act in the deformation of Fe and Ti alloys whereas dislocation flow units do not show any appreciable contribution. (5) The deformations of Fe and Ti alloys belong generally to pattern A (Case 1) and B (Case 2), respectively. (6) By applying the equations, f=$(1/{\alpha}_{g1}) sinh^-1({\beta}_{g1}{\dot{s}}$) and $f=(X_{g1}/{\alpha}_{g1})sinh^{-1}({\beta}_{g1}{\dot{s}})+ (X_{g2}/{\alpha}_{g2})\;shih^{-1}({\beta}_{g2}{\dot{s}})$ to the flow data of Fe and Ti alloys, the parametric values of $x_{gj}/{\alpha}_{gj}\;and\;{\beta}_{gs}(j=1\;or\;2)$ were determined, here the subscript g signifies a grain-boundary flow unit. (7) From the values of ($({\beta}_gj)^{-1}$) at different temperatures, the activation enthalpy ${\Delta}H_{gj}^{\neq}$ of deformation due to flow unit gj was determined, ($({\beta}_gj)^{-1}$) being proportional to , the jumping frequency (the rate constant) of flow unit gj. The ${\Delta}H_{gj}\;^{\neq}$ agreed very well with ${\Delta}H_{gj}\;^{\neq}$ (self-diff) of the element j whose diffusion in the sample is a critical step for the deformation as proposed by Kim-Ree's theory (Refer to Tables 3 and 4). (8) The fact, ${\Delta}H_{gj}\;^{\neq}={\Delta}H_{j}\;^{\neq}$ (self-diff), justifies the Kim-Ree theory and their method for determining activation enthalpies for deformation. (9) A linear relation between ${\beta}^{-1}$ and carbon content [C] in hot-rolled steel was observed, i.e., In ${\beta}^{-1}$ = -50.2 [C] - 40.3. This equation explains very well the experimental facts observed with regard to the deformation of hot-rolled steel..

Clustering and Comparative Analyses of Complete Genomes for the Elucidation of Evolutionary Characteristics

  • Kim, Jin-Sik;Lee, Sang-Yup
    • Proceedings of the Korean Society for Bioinformatics Conference
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    • 2005.09a
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    • pp.78-82
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    • 2005
  • Three of the genus Pseudomonas (P. aeruginosa, P. putida, P. syringae) show highly different phenotypic characteristics among them. Two of the three members are pathogenic and the other is non-pathogenic. Comparative analyses of the complete genomes can elucidate the genomic similarities and differences among them. We analyzed the three genomes and the genes of them to reveal the degree of conservation of chromosomes and similarity of the genes. The 2-dimensional dot plot between the pathogenic P. aeruginosa and non-pathogenic P. putida shared higher portion of the nucleotide sequences than other two combinations. Comparison of the nucleotide compositions by calculating the genome-scale plot of G+C contents and GC skew showed the variation of location. Comparison of the metabolic capabilities using the functional classification of KEGG orthology revealed that the differences in the number of genes for the specific functional categories resulted in the phenotypic differences. Finally combination of the analyses using the protein homologs supported the evolutionary distance of the P. putida obtained from other genome-scale comparisons.

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Comparative Analysis of the Three Classes of Archaeal and Bacterial Ribonucleotide Reductase from Evolutionary Perspective

  • Pangare, Meenal G.;Chandra, Sathees B.
    • Genomics & Informatics
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    • v.8 no.4
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    • pp.170-176
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    • 2010
  • The Ribonucleotide reductases (RNR) are essential enzymes that catalyze the conversion of nucleotides to deoxynucleotides in DNA replication and repair in all living organisms. The RNRs operate by a free radical mechanism but differ in the composition of subunit, cofactor required and regulation by allostery. Based on these differences the RNRs are classified into three classesclass I, class II and class III which depend on oxygen, adenosylcobalamin and S-adenosylmethionine with an iron sulfur cluster respectively for radical generation. In this article thirty seven sequences belonging to each of the three classes of RNR were analyzed by using various tools of bioinformatics. Phylogenetic analysis, dot-plot comparisons and motif analysis was done to identify a number of differences in the three classes of RNRs. In this research article, we have attempted to decipher evolutionary relationship between the three classes of RNR by using bioinformatics approach.

A study on the application of the aerial photographs for forest inventory (항공사진(航空寫眞)을 이용(利用)한 산림자원조사법(山林資源調査法)의 연구(硏究))

  • Kim, Kap Duk
    • Journal of Korean Society of Forest Science
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    • v.30 no.1
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    • pp.1-7
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    • 1976
  • This study was performed in Bo-Eun Gun, Chung-Cheong Buk Do. The forest types having been classified, the each area was measured by dot-grid method. The 820 sample points having been obtained by systematic sampling method, the tree heights, crown densities, crown diameters in the points were measured on the aerial photography, and the volumes per hectare were estimated by the comparison with stereogram. Thirty eight plots, which amounted to about 4.5% of all the sample points, were sampled with double sampling method and volume were measured by the ground survey method. the results were summarized as follows; 1. There is no significant differentia between the values measure by dot-grid method and the statistical values obtained by the authority for the area. 2. There is no significant differentia between the estimated values and the measured values for the volume. And the coefficient (b) was 1.18. 3. The heights of conifer trees were easily measured more or less, but it was some difficult for the deciduous trees, because the tops of trees were not observed easily. 4. All the values had a tendencies to be overestimated in the low stocked stand and to be underestimated in the high stocked stand. 5. When the aerial volume table method by ground checking needs to be used together, the work should be performed by the experienced technician and the photgraphic volume table should be made in advanced of the work.

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Immunostimulating Effect of 1,2-Benzopyrone on Phagocytic Response of Canine Peripheral Blood Phagocytes (개 말초혈액 탐식세포의 탐식반응에 대한 1,2-benzopyrone의 면역자극 효과)

  • 신정화;나기정;양만표
    • Journal of Veterinary Clinics
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    • v.21 no.1
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    • pp.23-28
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    • 2004
  • 1,2-benzopyrone has been shown to affect on the activation and stimulation of macrophage. To examine the immunostimulating effect of 1,2-benzopyrone on the phagocytic response of canine peripheral blood mononuclear cells (PBMC) as well as polymorphonuclear cells (PMN), the phagocytic activity of phagocytes was analyzed by flow cytometry system using FITC-labelled latex. The 1,2-benzopyrone did not show any direct effect on phagocytic response of PBMC and PMN. But it showed an enhanced effect on the phagocytic response of monocyte-rich cells fractioned by cell size from dot plot profile in flowcytometric cytography of PBMC. The phagocytic activity of these cells was also enhanced by addition of culture supernatant from PBMC treated with 1,2-benzopyrone. Similarly, the phagocytic activity of PMN but not PBMC in the same procedures was enhanced by culture supernatant from PBMC treated with 1,2-benzopyrone. However, the culture supernatant from PMN treated with 1.2-benzopyrone did not show the enhancing effect on phagocytic activity for monocyte-rich cells and PMN. These results, therefore, suggested that enhanced phagocytic activity of canine peripheral blood PMN and monocytes may be mainly mediated by humoral factor(S) released from PBMC treated with 1,2-benzopyrone.

A Comparative Analysis of Monofunctional Biosynthetic Peptidoglycan Transglycosylase (MBPT) from Pathogenic and Non-pathogenic Bacteria

  • Baker, Andrew T.;Takahashi, Natsumi;Chandra, Sathees B.
    • Genomics & Informatics
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    • v.8 no.2
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    • pp.63-69
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    • 2010
  • Monofunctional biosynthetic peptidoglycan transglycosylase (MBPT) catalyzes the formation of the glycan chain in bacterial cell walls from peptidoglycan subunits: N-acetylglucosamine (NAG) and acetylmuramic acid (NAM). Bifunctional glycosyltransferases such as the penicillin binding protein (PBP) have peptidoglycan glycosyltransferase (PGT) on their C terminal end which links together the peptidoglycan subunits while transpeptidase (TP) on the N terminal end cross-links the peptide moieties on the NAM monosaccharide of the peptide subunits to create the bacterial cell wall. The singular function of MBPT resembles the C terminal end of PBP as it too contains and utilizes a similar PGT domain. In this article we analyzed the infectious and non infectious protein sequences of MBPT from 31 different strains of bacteria using a variety of bioinformatic tools. Motif analysis, dot-plot comparison, and phylogenetic analysis identified a number of significant differences between infectious and non-infectious protein sequences. In this paper we have made an attempt to explain, analyze and discuss these differences from an evolutionary perspective. The results of our sequence analysis may open the door for utilizing MBPT as a new target to fight a variety of infectious bacteria.

DEVELOPMENT OF STATEWIDE TRUCK TRAFFIC FORECASTING METHOD BY USING LIMITED O-D SURVEY DATA (한정된 O-D조사자료를 이용한 주 전체의 트럭교통예측방법 개발)

  • 박만배
    • Proceedings of the KOR-KST Conference
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    • 1995.02a
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    • pp.101-113
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    • 1995
  • The objective of this research is to test the feasibility of developing a statewide truck traffic forecasting methodology for Wisconsin by using Origin-Destination surveys, traffic counts, classification counts, and other data that are routinely collected by the Wisconsin Department of Transportation (WisDOT). Development of a feasible model will permit estimation of future truck traffic for every major link in the network. This will provide the basis for improved estimation of future pavement deterioration. Pavement damage rises exponentially as axle weight increases, and trucks are responsible for most of the traffic-induced damage to pavement. Consequently, forecasts of truck traffic are critical to pavement management systems. The pavement Management Decision Supporting System (PMDSS) prepared by WisDOT in May 1990 combines pavement inventory and performance data with a knowledge base consisting of rules for evaluation, problem identification and rehabilitation recommendation. Without a r.easonable truck traffic forecasting methodology, PMDSS is not able to project pavement performance trends in order to make assessment and recommendations in the future years. However, none of WisDOT's existing forecasting methodologies has been designed specifically for predicting truck movements on a statewide highway network. For this research, the Origin-Destination survey data avaiiable from WisDOT, including two stateline areas, one county, and five cities, are analyzed and the zone-to'||'&'||'not;zone truck trip tables are developed. The resulting Origin-Destination Trip Length Frequency (00 TLF) distributions by trip type are applied to the Gravity Model (GM) for comparison with comparable TLFs from the GM. The gravity model is calibrated to obtain friction factor curves for the three trip types, Internal-Internal (I-I), Internal-External (I-E), and External-External (E-E). ~oth "macro-scale" calibration and "micro-scale" calibration are performed. The comparison of the statewide GM TLF with the 00 TLF for the macro-scale calibration does not provide suitable results because the available 00 survey data do not represent an unbiased sample of statewide truck trips. For the "micro-scale" calibration, "partial" GM trip tables that correspond to the 00 survey trip tables are extracted from the full statewide GM trip table. These "partial" GM trip tables are then merged and a partial GM TLF is created. The GM friction factor curves are adjusted until the partial GM TLF matches the 00 TLF. Three friction factor curves, one for each trip type, resulting from the micro-scale calibration produce a reasonable GM truck trip model. A key methodological issue for GM. calibration involves the use of multiple friction factor curves versus a single friction factor curve for each trip type in order to estimate truck trips with reasonable accuracy. A single friction factor curve for each of the three trip types was found to reproduce the 00 TLFs from the calibration data base. Given the very limited trip generation data available for this research, additional refinement of the gravity model using multiple mction factor curves for each trip type was not warranted. In the traditional urban transportation planning studies, the zonal trip productions and attractions and region-wide OD TLFs are available. However, for this research, the information available for the development .of the GM model is limited to Ground Counts (GC) and a limited set ofOD TLFs. The GM is calibrated using the limited OD data, but the OD data are not adequate to obtain good estimates of truck trip productions and attractions .. Consequently, zonal productions and attractions are estimated using zonal population as a first approximation. Then, Selected Link based (SELINK) analyses are used to adjust the productions and attractions and possibly recalibrate the GM. The SELINK adjustment process involves identifying the origins and destinations of all truck trips that are assigned to a specified "selected link" as the result of a standard traffic assignment. A link adjustment factor is computed as the ratio of the actual volume for the link (ground count) to the total assigned volume. This link adjustment factor is then applied to all of the origin and destination zones of the trips using that "selected link". Selected link based analyses are conducted by using both 16 selected links and 32 selected links. The result of SELINK analysis by u~ing 32 selected links provides the least %RMSE in the screenline volume analysis. In addition, the stability of the GM truck estimating model is preserved by using 32 selected links with three SELINK adjustments, that is, the GM remains calibrated despite substantial changes in the input productions and attractions. The coverage of zones provided by 32 selected links is satisfactory. Increasing the number of repetitions beyond four is not reasonable because the stability of GM model in reproducing the OD TLF reaches its limits. The total volume of truck traffic captured by 32 selected links is 107% of total trip productions. But more importantly, ~ELINK adjustment factors for all of the zones can be computed. Evaluation of the travel demand model resulting from the SELINK adjustments is conducted by using screenline volume analysis, functional class and route specific volume analysis, area specific volume analysis, production and attraction analysis, and Vehicle Miles of Travel (VMT) analysis. Screenline volume analysis by using four screenlines with 28 check points are used for evaluation of the adequacy of the overall model. The total trucks crossing the screenlines are compared to the ground count totals. L V/GC ratios of 0.958 by using 32 selected links and 1.001 by using 16 selected links are obtained. The %RM:SE for the four screenlines is inversely proportional to the average ground count totals by screenline .. The magnitude of %RM:SE for the four screenlines resulting from the fourth and last GM run by using 32 and 16 selected links is 22% and 31 % respectively. These results are similar to the overall %RMSE achieved for the 32 and 16 selected links themselves of 19% and 33% respectively. This implies that the SELINICanalysis results are reasonable for all sections of the state.Functional class and route specific volume analysis is possible by using the available 154 classification count check points. The truck traffic crossing the Interstate highways (ISH) with 37 check points, the US highways (USH) with 50 check points, and the State highways (STH) with 67 check points is compared to the actual ground count totals. The magnitude of the overall link volume to ground count ratio by route does not provide any specific pattern of over or underestimate. However, the %R11SE for the ISH shows the least value while that for the STH shows the largest value. This pattern is consistent with the screenline analysis and the overall relationship between %RMSE and ground count volume groups. Area specific volume analysis provides another broad statewide measure of the performance of the overall model. The truck traffic in the North area with 26 check points, the West area with 36 check points, the East area with 29 check points, and the South area with 64 check points are compared to the actual ground count totals. The four areas show similar results. No specific patterns in the L V/GC ratio by area are found. In addition, the %RMSE is computed for each of the four areas. The %RMSEs for the North, West, East, and South areas are 92%, 49%, 27%, and 35% respectively, whereas, the average ground counts are 481, 1383, 1532, and 3154 respectively. As for the screenline and volume range analyses, the %RMSE is inversely related to average link volume. 'The SELINK adjustments of productions and attractions resulted in a very substantial reduction in the total in-state zonal productions and attractions. The initial in-state zonal trip generation model can now be revised with a new trip production's trip rate (total adjusted productions/total population) and a new trip attraction's trip rate. Revised zonal production and attraction adjustment factors can then be developed that only reflect the impact of the SELINK adjustments that cause mcreases or , decreases from the revised zonal estimate of productions and attractions. Analysis of the revised production adjustment factors is conducted by plotting the factors on the state map. The east area of the state including the counties of Brown, Outagamie, Shawano, Wmnebago, Fond du Lac, Marathon shows comparatively large values of the revised adjustment factors. Overall, both small and large values of the revised adjustment factors are scattered around Wisconsin. This suggests that more independent variables beyond just 226; population are needed for the development of the heavy truck trip generation model. More independent variables including zonal employment data (office employees and manufacturing employees) by industry type, zonal private trucks 226; owned and zonal income data which are not available currently should be considered. A plot of frequency distribution of the in-state zones as a function of the revised production and attraction adjustment factors shows the overall " adjustment resulting from the SELINK analysis process. Overall, the revised SELINK adjustments show that the productions for many zones are reduced by, a factor of 0.5 to 0.8 while the productions for ~ relatively few zones are increased by factors from 1.1 to 4 with most of the factors in the 3.0 range. No obvious explanation for the frequency distribution could be found. The revised SELINK adjustments overall appear to be reasonable. The heavy truck VMT analysis is conducted by comparing the 1990 heavy truck VMT that is forecasted by the GM truck forecasting model, 2.975 billions, with the WisDOT computed data. This gives an estimate that is 18.3% less than the WisDOT computation of 3.642 billions of VMT. The WisDOT estimates are based on the sampling the link volumes for USH, 8TH, and CTH. This implies potential error in sampling the average link volume. The WisDOT estimate of heavy truck VMT cannot be tabulated by the three trip types, I-I, I-E ('||'&'||'pound;-I), and E-E. In contrast, the GM forecasting model shows that the proportion ofE-E VMT out of total VMT is 21.24%. In addition, tabulation of heavy truck VMT by route functional class shows that the proportion of truck traffic traversing the freeways and expressways is 76.5%. Only 14.1% of total freeway truck traffic is I-I trips, while 80% of total collector truck traffic is I-I trips. This implies that freeways are traversed mainly by I-E and E-E truck traffic while collectors are used mainly by I-I truck traffic. Other tabulations such as average heavy truck speed by trip type, average travel distance by trip type and the VMT distribution by trip type, route functional class and travel speed are useful information for highway planners to understand the characteristics of statewide heavy truck trip patternS. Heavy truck volumes for the target year 2010 are forecasted by using the GM truck forecasting model. Four scenarios are used. Fo~ better forecasting, ground count- based segment adjustment factors are developed and applied. ISH 90 '||'&'||' 94 and USH 41 are used as example routes. The forecasting results by using the ground count-based segment adjustment factors are satisfactory for long range planning purposes, but additional ground counts would be useful for USH 41. Sensitivity analysis provides estimates of the impacts of the alternative growth rates including information about changes in the trip types using key routes. The network'||'&'||'not;based GMcan easily model scenarios with different rates of growth in rural versus . . urban areas, small versus large cities, and in-state zones versus external stations. cities, and in-state zones versus external stations.

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