Inferring Protein Function from Homology Using the Princeton Protein Orthology Database (P‐POD)

Inferring a protein's function by homology is a powerful tool for biologists. The Princeton Protein Orthology Database (P‐POD) offers a simple way to visualize and analyze the relationships between homologous proteins in order to infer function. P‐POD contains computationally generated analysis distinguishing orthologs from paralogs combined with curated published information on functional complementation and on human diseases. P‐POD also features an applet, Notung, for users to explore and modify phylogenetic trees and generate their own ortholog/paralogs calls. This unit describes how to search P‐POD for precomputed data, how to find and use the associated curated information from the literature, and how to use Notung to analyze and refine the results.Curr. Protoc. Bioinform. 33:6.11.1‐6.11.12. © 2011 by John Wiley & Sons, Inc.