PROMPT: a protein mapping and comparison tool

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Document Type Definition (DTD) of PROMPT's generic XML format

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Screenshot of the PROMPT web page. Here, we provide the latest news and PROMPT versions along with useful information. Additionally, all case studies shown in this paper including the underlying data are freely available as detailed work-through tutorials.

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Built-in help system. Comprehensive and intelligent online help with example data and a demonstration workspace allows easy usage of PROMPT without prior knowledge.

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Binning wizard for setting up interval borders. A. First dialog page. The user can either let PROMPT automatically estimate the interval borders, of specify a fixed interval width or the number of intervals. The selected options shown create histogram intervals that have a width of 1, no decimal places, and the range from 6 to 21. B. Optional second dialog page. Here the proposed binning can be previewed and altered. Note that we used the special keywords -INF and +INF for negative and positive infinity in the first and last interval to specify that all values less than 7 or higher than 20 fall into these bins.

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Example of a built-in interactive scatter plot. Protein length of E.coli lysate proteins is plotted against their hydrophobicity. The Pearson correlation coefficient is -0.69 with a p-value of 2.8E-54. By pressing and holding the left mouse button it is possible to zoom in the desired area. Clicking on an individual point on the plot leads to numeric values associated with this point being displayed.

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Usage of derived sequence based properties in a generic analysis of PROMPT. Here the isoelectric point (pI) distributions of the E.coli lysate and membrane proteins are compared using the numeric comparison method. PROMPT calculates the pI values automatically if protein sequences are available.

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Screenshots of PROMPT's visualisations of the sequence based symbol analysis methods. In this example we compared two protein sets with respect of their amino acid composition. The positive and the negative datasets are constituted by the proteins known to crystallize and the proteins whose structure was only resolved by NMR, respectively (Smialowski et al., 2005). A. Here the frequencies of each amino acid in both proteins are plotted. For example: a frequency of 5% for threonine in the positive protein dataset means that out of all residues 5% are T's. B. Using the same data as in A, here the frequency differences of all sequence elements are shown. For example, the positive value of 0.5% for Y means that this amino acid is about a half percent more frequent is the first dataset. Bars with red color have a significant p-value according to the Mann-Whitney test. C. Additionally the frequency distributions of all amino acids can be shown as box plots as exemplified by cysteine here. D. Complementary to a box plot depiction PROMPT provides histogram visualizations.

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