Bioinformatics Web Tool Aids Functional Annotation of Plant and Microbial Genomes


Gene sequencing has become very fast and inexpensive, yet the bottleneck of producing reliable functional annotations of gene sequences remains a challenge. Functional annotations commonly use a protocol based on pairwise sequence comparison algorithms such as the Basic Local Alignment Search Tool (BLAST). However, these methods can miss important phylogenetic relationships such as orthology. Phylogenetic methods that explicitly reconstruct evolutionary relationships in multigene families have a higher precision for whole genome functional annotation. A new phylogenetic web server and analysis platform, PhyloFacts, integrates experimental and annotation data from different resources including SwissProt, Gene Ontology, Pfam, BioCyc, Enzyme Commission, and third-party orthology databases. These data are then used to provide functional annotations for user-inputted protein sequences. PhyloFacts also allows users to drill down and view provenance and supporting data for functional annotations. PhyloFacts makes use of Hidden Markov Model (HMM) algorithms to place user-submitted sequences into precalculated phylogenetic relationships, or trees. As a result, its functional subclassifications have greater precision when compared with other orthology web services. Funding for PhyloFacts was provided as part of the Department of Energy’s Systems Biology Knowledgebase (KBase) enabling tools program and will be a component of future KBase services.


Afrasiabi, C., B. Samad, D. Dineen, C. Meacham, and K. Sjölander. 2013. “The PhyloFacts FAT-CAT Web Server: Ortholog Identification and Function Prediction Using Fast Approximate Tree Classification,” Nucleic Acids Research, 1–7. DOI: 10.1093/nar/gkt399.