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Figure 3 | BMC Bioinformatics

Figure 3

From: Visualising biological data: a semantic approach to tool and database integration

Figure 3

The Utopia suite. Screenshot of selected tools from the Utopia suite, as used in the Case Study: top left shows Utopia's search tool, having located a number of rhodopsin sequences in UniProt; the bottom image illustrates the Sequences alignment editor, in which sequences selected from the search results have been automatically aligned – highlighted are two manually-selected TM domains (denoted by the green bars), contrasting the results from two TM-prediction tools (denoted by the pink and blue hatched bars) with the known locations of the TM helices from the crystal structure of bovine rhodopsin (green zigzags); centre right shows the Structures tool, depicting the 3D structure of rhodopsin, with the manually-selected TM domains highlighted in green; beneath this is shown the PRECIS report, providing relevant literature citations, database cross references, details of the protein function, disease associations, and so on. Used in this way, the efficacy of the TM prediction tools relative to the known structure is striking.

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