Related Experiment Video
Updated: May 4, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
POGs2: a web portal to facilitate cross-species inferences about protein architecture and function in plants
Michael Tomcal1, Nicholas Stiffler, Alice Barkan
1Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America.
Abstract:
The Putative orthologous Groups 2 Database (POGs2) (http://pogs.uoregon.edu/) integrates information about the inferred proteomes of four plant species (Arabidopsis thaliana, Zea mays, Orza sativa, and Populus trichocarpa) in a display that facilitates comparisons among orthologs and extrapolation of annotations among species. A single-page view collates key functional data for members of each Putative Orthologous Group (POG): graphical representations of InterPro domains, predicted and established intracellular locations, and imported gene descriptions. The display incorporates POGs predicted by two different algorithms as well as gene trees, allowing users to evaluate the validity of POG memberships. The web interface provides ready access to sequences and alignments of POG members, as well as sequences, alignments, and domain architectures of closely-related paralogs. A simple and flexible search interface permits queries by BLAST and by any combination of gene identifier, keywords, domain names, InterPro identifiers, and intracellular location. The concurrent display of domain architectures for orthologous proteins highlights errors in gene models and false-negatives in domain predictions. The POGs2 layout is also useful for exploring candidate genes identified by transposon tagging, QTL mapping, map-based cloning, and proteomics, and for navigating between orthologous groups that belong to the same gene family.
Related Concept Videos
Cell Signaling in Plants
Protein-protein Interfaces
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Transport to the Inner Chloroplast Membrane
Protein Organization
The primary structure of a protein is its amino acid sequence....

