系统发育树
亚科
注释
树(集合论)
计算机科学
本体论
软件
情报检索
计算生物学
人工智能
生物
基因
遗传学
程序设计语言
认识论
数学分析
哲学
数学
作者
Haiming Tang,Alex Bateman,Paul D. Thomas
出处
期刊:Bioinformatics
[Oxford University Press]
日期:2018-07-19
卷期号:35 (3): 518-520
被引量:21
标识
DOI:10.1093/bioinformatics/bty625
摘要
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. Availability and implementation TreeGrafter is freely available on the web at https://github.com/pantherdb/TreeGrafter, including as a Docker image. Supplementary information Supplementary data are available at Bioinformatics online.
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