NAViGaTOR Protein-protein interaction networks visualization software.
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analyzer analysis view

NAViGaTOR Description

NAViGaTOR is a handy, easy to use application specially designed to help you visualize and analyze protein-protein interaction networks. NAViGaTOR can query OPHID / I2D - online databases of interaction data - and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. This tool also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI). Main features: NAViGaTOR combines a visualization system implemented in OpenGL with a graphical user interface and analytical algorithms implemented in Java. Networks can be loaded from a file (tab-delimited, NAViGaTOR XML, BioPAX or PSI formats), or can be generated dynamically by executing a visual query to OPHID / I2D (Interologous Interaction Database -- an online database of known, HTP, and predicted protein-protein interactions for human, rat, mouse, fly, worm, and yeast) or cPath. The NAViGaTOR workspace supports multiple network panels which can be manipulated by cutting, copying and pasting nodes and edges. Networks can be exported in tab-delimited, NAViGaTOR XML, PSI, or Pajek formats, and multiple graphical formats (BMP, JPG, TIFF, SVG, PDF). Networks can be viewed in 2D and 3D. Nodes can be positioned using a mixture of automatic force-directed layout and manual placement. One of the automatic layout algorithms used is a multi-level force-directed layout algorithm called GRIP (Graph dRawing with Intelligent Placement) . Because of the nearly linear time complexity of GRIP, NAViGaTOR can visualize full interactomes from I2D. Subnetworks that are highly interconnected, and nodes that are hubs (i.e. that interact with many other nodes), can be automatically identified to aid analysis. Groups of nodes can be collapsed into composite nodes, either manually, or in an automated fashion. Subsets of a network can be bookmarked and manipulated using standard set operations, such as union, intersection and difference. The opacity of nodes and edges can be adjusted to change the contrast of elements in the network and emphasize selected elements.

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