Phylogenomic analysis of protein or gene function is a form of functional genomics, designed to improve the accuracy of predicted molecular function by integrating evolutionary tree construction and analysis in the annotation pipeline.  We combine phylogenomic approaches with protein structure prediction to elucidate the correlation between changes in protein structure and changes in molecular function.

Principal directions:

• Algorithm development for protein functional, structural and phylogenetic analysis.
• Algorithm deployment in collaboration with experimental biologists.
• Phylogenomic analysis platform development for the scientific community.

New in PhyloFacts

12 October 2007.  Sequence Search now includes automatic classification to protein subfamilies. Protein subfamilies, identified by the SCI-PHY algorithm, correspond closely to functional subtypes defined by experts and to conserved clades found by phylogenetic analysis.

Quickstart guide to using this resource

1. See if your protein of interest can be classified to ("matches") one or more PhyloFacts protein families/subfamilies:
   • Go to PhyloFacts > Sequence Search. 
   • Paste in your protein sequence and click "submit".
   • You can click "Check progress" to see if results are ready, or wait for an email (it should only be a minute!).
   • Results include "protein map" diagrams, showing where PhyloFacts protein families or subfamilies align to ("match") your protein. Click on the protein family or subfamily names to see more information about those PhyloFacts protein families.
2. Create your own PhyloFacts protein family, using your protein of interest as the "seed" to identify family members, create an alignment, perform subfamily classification, and create phylogenetic trees:
   • Go to Tools > PhyloBuilder. 
   • Paste in your protein sequence and click "submit".
   • You can click "Check progress" to see if results are ready, or wait for an email (depending on how many family members are found, it can take from a few minutes to about a half-hour).
   • Results include a phylogenetic tree and potential homologous solved structures. Click on the "Tree viewer" icon — look for your sequence (identified as "seed") in the tree to explore its "neighbors." Click on the "3D structure" icon to view potential homologous structures and family and subfamily significant residues — amino-acids that are conserved and that may represent catalytic or binding sites.