TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations.

Journal: Bioinformatics (Oxford, England)
Published Date: Feb 1, 2019

Abstract

SUMMARY: TreeGrafter is a new software tool for annotating protein sequences using pre-annotated phylogenetic trees. Currently, the tool provides annotations to Gene Ontology (GO) terms, and PANTHER family and subfamily. The approach is generalizable to any annotations that have been made to internal nodes of a reference phylogenetic tree. TreeGrafter takes each input query protein sequence, finds the best matching homologous family in a library of pre-calculated, pre-annotated gene trees, and then grafts it to the best location in the tree. It then annotates the sequence by propagating annotations from ancestral nodes in the reference tree. We show that TreeGrafter outperforms subfamily HMM scoring for correctly assigning subfamily membership, and that it produces highly specific annotations of GO terms based on annotated reference phylogenetic trees. This method will be further integrated into InterProScan, enabling an even broader user community.

Authors

  • Haiming Tang
    Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA.
  • Robert D Finn
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
  • Paul D Thomas
    Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA and.

Keywords

External Resources

Popular Topics
Recent Journals