Mountain plot

Fig. 12.1. Dot plot, secondary structure graph, and mountain plot for die example sequence...

The resulting plot shows three curves two mountain plots derived from the MFE structure and the pairing probabilities and a positional entropy curve. Well-defined regions are identified by low entropy. By superimposing several mountain plots, structures can easily be compared. 

A modification of the histogram display of differences is a plot suggested by Krouwer and Mont)P Icnown as the mountain plot. This is a plot of cumulative frequencies (c/%) of differences up to 50% with subsequent subtracted cumulative frequencies (100% - cf%). Such a plot shows in principle the same information as a histogram or frequency polygon plot. An advantage may be that the percentiles can be directly read from the plot. 

Yet another useful representation of RNA structures is the mountain plot. In the mountain plot a pair (i, j) is represented by a colored trapez with baseline from position i to position j and height proportional to the probability. The command... 

Identify the conserved region from the dot plot or mountain plot and write a new alignment file for each of them. The clustalx program is convenient for cutting a region out of an alignment, but a simple text editor can be used as well. 

In optimizing a method, we seek to find the combination of experimental parameters producing the best result or response. We can visualize this process as being similar to finding the highest point on a mountain, in which the mountain s topography, called a response surface, is a plot of the system s response as a function of the factors under our control. 

Figure 1. Map of the Burrows Trail on the southwest-facing slope of Camels Hump mountain showing location of permanently-marked study plots.

PCA components with small variances may only reflect noise in the data. Such a plot looks like the profile of a mountain after a steep slope a more flat region appears that is built by fallen, deposited stones (called scree). Therefore, this plot is often named scree plot so to say, it is investigated from the top until the debris is reached. However, the decrease of the variances has not always a clear cutoff, and selection of the optimum number of components may be somewhat subjective. Instead of variances, some authors plot the eigenvalues this comes from PCA calculations by computing the eigenvectors of the covariance matrix of X note, these eigenvalues are identical with the score variances. 

Mossbauer spectrum spect A plot of the absorption, by nuclei bound in a crystal lattice, of gamma rays emitted by similar nuclei in a second crystal, as a function of the relative velocity of the two crystals. mus.bau-or. spek-trom mountain blue inorgchem 2CuC03-Cu(0H >2 Ground azurite used as a paint pigment. 

Measurements from a downtown site in Frankfurt-am-Main and another on a nearby 800-m mountain, Kleiner Feldberg, both in the Federal Republic of Germany, are plotted in Figure 4-1. As opposed to the pattern in New York State," the ozone concentration at the urban... 

Fig. 16.7 Plutonium L -edge XANES spectra plotted with respect to the relative XANES edge energy for sorbed Pu on Yucca Mountain tuff at 6 months and 2 years. All spectra taken after two years indicated an average oxidation state of Pu(IV) those taken after 6 months had average oxidation states predominantly of Pu(V) and Pu(VI). Reprinted with permission from Powell BA, Duff MC, Kaplan DI, Field RA, Newville M, Hunter BD, Bertsch PM, Coates JT, Serkiz SM, Sutton RS, Triay IR, Vaniman DT (2006) Plutonium oxidation and subsequent reduction by Mn(IV) minerals in Yucca Mountain tuff. Environ Sci Technol 40 3508-3514. Copyright 2006 American Chemical Society...

The two-dimensional matrix can be recorded by an analog plotter, or much faster by a digital plotter or a graphic display. Stacked plots as drawn in Fig. 2.50(d) can be obtained, providing a panoramic picture of the carbon-13 signals (3) and their individual multiplets (JCHj. Useful for practical evaluation, the contour plot is like a contour map of the signal mountains, giving a type of aerial view of the CH multiplets (Fig. 2.50(e)). 

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