PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification

Table 2 Comparison of PhyloFacts with other functional classification resources

Analysis of user-submitted sequences
	PhyloFacts	Panther	TIGRFAMs	Sanger PFAM	SMART	InterPro	Superfamily
Classification to full-length protein families	Yes	No*	Yes
Subfamily level classification	Yes	Yes	Yes
Domain level classification	Yes		Yes	Yes	Yes	Yes	Yes
DNA sequence analysis	Yes			Yes		Yes	Yes
Batch-mode sequence inputs allowed	Yes			Yes	Yes		Yes
Analysis required for phylogenomic inference
Clusters based on full-length protein families	Yes	No*	Yes
Phylogenetic trees for full-length protein families	Yes
Subfamily identification	Yes	Yes	Yes			Partial^†
GO data for individual sequences	Yes	No^‡				Yes
GO data for clusters	Yes	No^‡	Yes	Yes	Yes	Yes
GO evidence codes	Yes					Yes
EC numbers for individual sequences	Yes	Yes	Yes
EC numbers for each cluster	Yes		Yes
Taxonomy information	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Analyses required for function inference based on structure
Phylogenetic trees for single domains	Yes			Yes
Clusters based on domains	Yes		Yes	Yes	Yes	Yes	Yes
Predicted three-dimensional structure for a protein family	Yes			Yes	Yes	Yes	Yes
Predicted critical residues	Yes
PDB structure visualization	Yes			Yes
PFAM domains	Yes		Yes	Yes	Yes	Yes
Transmembrane domain prediction	Yes				Yes	Yes
Signal peptide prediction	Yes				Yes	Yes
SCOP classification	Yes			Yes	Yes	Yes	Yes
Links to PDB	Yes			Yes	Yes	Yes
Additional protein family data
Retrieval of relevant literature for individual families	Partial	Yes	Yes	Yes	Yes	Yes
Extended protein family annotation		Yes		Yes	Yes	Yes
Clusters of interacting domain families				Yes
Graphic displays of related domain architectures				Yes	Yes	Yes	Yes

This table compares the functionalities provided by PhyloFacts with those of standard functional classification resources for structural phylogenomic analysis. PhyloFacts is the only online resource that enables structural phylogenomic inference of protein function, including clustering of sequences into structural equivalence classes (that is, containing the same domain architecture), construction of phylogenetic trees, identification of functional subfamilies, subfamily hidden Markov models and structure prediction. This differentiates PhyloFacts from other resources that almost exclusively enable domain prediction (for example PFAM, Superfamily) and those such as TIGRFAMs that cluster full-length protein sequences but do not integrate structural and phylogenomic analysis. Reported as of May 2006. *Although Panther asserts that its families contain globally alignable sequences, this is not always the case (see additional data file 1 for details). ^†InterPro has defined parent/child relationships between some entries that are considered equivalent of family/subfamily relationships. But these are not defined for every cluster. ^‡Panther provides its own ontology terms instead of the standard GO annotations. Links to the resources used for this comparison: PhyloFacts Resource [11]; Celera Genomics Panther Classification [74]; TIGRFAMs [75]; PFAM HMM library at the Sanger Institute [76]; SMART [77]; InterPro [78]; Superfamily [79].

ISSN: 1474-760X