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Table 2 Comparison of PhyloFacts with other functional classification resources

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

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
  1. 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].