A detailed step-by-step tutorial is available here.
The PHOG webserver provides a way of retrieving pre-calculated super-orthology
groups for sequences in the PhyloFacts resource
PhyloFacts is an encyclopedia of thousands of protein families from across the
Tree of Life, including phylogenetic trees, predicted subfamilies, family and
subfamily hidden Markov models, predicted 3D structures, GO annotations and
links to external resources. PHOGs are derived by analysis of phylogenetic
trees for PhyloFacts families, and correspond to super-orthology groups found
in these trees.
If you use PHOG, please cite the following paper which describes it:
PhyloFacts is described in the following papers:
Krishnamurthy, Brown, Kirshner and Sjölander, "PhyloFacts: An online
structural phylogenomic encyclopedia for protein functional and structural
classification," Genome Biology 2006
Glanville, Kirshner, Krishnamurthy and Sjölander, "Berkeley Phylogenomics
Group web servers: resources for structural phylogenomic analysis,"
Nucleic Acids Research 2007
Step 1: Type (or paste) in a protein sequence identifier or accession. See examples and details of accepted inputs.
Step 2: Click “Search”. Results will display within a few seconds on the page below.
If your input sequence is contained in a PhyloFacts orthology group, two
tables will be displayed. The first, "PhyloFacts Orthology Groups Containing
the Query Sequence", gives a list of orthology groups, with summary data and
links to each PHOG page. The second table, "Orthologs and In-Species
Paralogs from One or More PhyloFacts Families", gives a list of orthologs,
retrieved from the orthology groups listed in the first table.
Orthologs and In-Species Paralogs from One or More PhyloFacts Families
Gene: UniProt accession. Clicking on this link will bring you to the corresponding page in the UniProt resource.
Species: The species of origin.
UniProt ID: The identifier for the sequence.
Description: A description of the molecular function of the protein, drawn from the UniProt resource.
Links to other resources: The next five columns include icons displaying links to external resources where available: SwissProt, Gene Ontology and biological literature links in the UniProt resource, and KEGG and BioCyc pathway data.
Protein-protein interactions: Link to information about interactions between this and other proteins.
Alignment: PhyloFacts families are of various types, depending on the degree of alignment overlap. There are three basic types: Domain (sequences share a common structural domain), Global (sequences align along their entire lengths), and Local (local alignments with no correspondence to a solved structure). Orthologs defined within Global Homology Group families are more likely to have a common function than those that share only a local region of homology.
PHOG: the accession for the PhyloFacts orthology group.
EC: a link to the IntEnz database at the EBI (http://www.ebi.ac.uk/intenz/)
providing information about Enzyme Commission numbers.