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arXiv · 1802.07304

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

Haiming Tang·Robert D Finn·Paul D Thomas
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Abstract

Summary: TreeGrafter is a new software tool for annotating protein sequences using annotated phylogenetic trees. Cur-rently, the tool provides annotations to Gene Ontology terms, and PANTHER protein class, family and subfamily. The ap-proach is generalizable to any annotations that have been made to internal nodes of a reference phylogenetic tree. Tree-Grafter 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 anno-tations from its ancestral nodes in the reference tree. We show that TreeGrafter outperforms subfamily HMM scoring for cor-rectly assigning subfamily membership, and that it produces highly specific annotations of GO terms based on annotated reference phylogenetic trees. This method will be further inte-grated into InterProScan, enabling an even broader user com-munity. Availability: TreeGrafter is freely available on the web at https://github.com/haimingt/TreeGrafting.

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BibTeXRIS

Haiming Tang, Robert D Finn, Paul D Thomas. 2018-02-20. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. https://arxiv.org/abs/1802.07304

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