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Section: New Software and Platforms
family-3d
Keywords: Biodiversity - Point cloud - 3D modeling
Scientific Description: The method statistically selects a subset of pairwise distances between proteins in the family, constructs a weighted graph, and lays it out using an adaptation of the three-dimensional extension of the Kamada-Kawai force-directed layout.
Functional Description: Family-3D lays out high-dimension protein family point clouds in 3D space. The resulting lower-dimension forms can be printed, so that they can be explored and compared manually. They can also be explored interactively or stereographically.
Comparison of the 3D forms reveals classes of structurally similar families, whose characteristic shapes correspond to different evolutionary scenarios. Some of these scenarios are: neofunctionalization, subfunctionalization, founder gene effect, ancestral family.
To facilitate curator training, Family-3D includes an interactive terminal containing a microcontroller, an RFID reader, and an LED ring. A set of shapes that fall in predetermined classes is printed, with a unique RFID tag in each shape. Trainees classify family shapes by manual inspection and submit their classes to the terminal, which evaluates the proposed class and provides visual feedback.