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NAR Molecular Biology Database Collection entry number 981
Krishnamurthy N., Brown D., Kirshner D., Glanville J. and SjÖlander K.
Dept. of Bioengineering, University of California, Berkeley, CA, USA

Database Description

The PhyloFacts resource contains pre-calculated structural and phylogenomic analysis of over 15,000 protein family "books" across the Tree of Life. Each book includes a multiple sequence alignment, one or more phylogenetic trees, predicted subfamilies, predicted 3D protein structures, active sites and other key residues, cellular localization, and Gene Ontology (GO) annotations and evidence codes. PhyloFacts includes hidden Markov models for classification of user-submitted (DNA or protein) sequences to protein families and subfamilies. Our current focus is on covering all the gene families represented in the human genome and all structural domains, but plan to expand the resource to include all proteins in all species. PhyloFacts enables biologists to avoid the systematic errors associated with function prediction by homology through the integration of a variety of experimental data and bioinformatics methods in an evolutionary framework.


This work was supported by a Presidential Early Career Award for Scientists and Engineers (PECASE) from the National Science Foundation, and by an RO1 from the National Human Genome Research Institute of the NIH.


1. Krishnamurthy, N., Brown, D., Kirshner, D. and Sjölander, K. (2006). PhyloFacts: An online structural phylogenomic encyclopedia for protein functional and structural classification. Genome Biology, 7(9):R83.

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