Unit

UNIT 6.11 Inferring Protein Function from Homology Using the Princeton Protein Orthology Database (P-POD)

  1. Michael S. Livstone1,
  2. Rose Oughtred1,
  3. Sven Heinicke1,
  4. Benjamin Vernot2,3,
  5. Curtis Huttenhower4,
  6. Dannie Durand2,5,
  7. Kara Dolinski1

Published Online: 1 MAR 2011

DOI: 10.1002/0471250953.bi0611s33

Lab Protocol Title

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

Additional Information

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.

Author Information

  1. 1

    Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey

  2. 2

    Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania

  3. 3

    Currently at the Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington

  4. 4

    Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts

  5. 5

    Department of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania

Publication History

  1. Published Online: 1 MAR 2011
  2. Published Print: MAR 2011
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Abstract

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.

Keywords:

  • functional complementation;
  • disease;
  • conservation;
  • phylogenetic analysis;
  • trees;
  • paralogs;
  • Notung
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