UNIT 6.11 Inferring Protein Function from Homology Using the Princeton Protein Orthology Database (P-POD)
Published Online: 1 MAR 2011
Copyright © 2011 by John Wiley & Sons, Inc.
Lab Protocol Title
Current Protocols in Bioinformatics
How to Cite
Livstone, M. S., Oughtred, R., Heinicke, S., Vernot, B., Huttenhower, C., Durand, D. and Dolinski, K. 2011. Inferring Protein Function from Homology Using the Princeton Protein Orthology Database (P-POD). Current Protocols in Bioinformatics. 33:6.11:6.11.1–6.11.12.
- Published Online: 1 MAR 2011
- Published Print: MAR 2011
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.
- functional complementation;
- phylogenetic analysis;