{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T20:09:10Z","timestamp":1776197350157,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2018,7,19]],"date-time":"2018-07-19T00:00:00Z","timestamp":1531958400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Science Foundation","award":["1458808"],"award-info":[{"award-number":["1458808"]}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BB\/N00521X\/1"],"award-info":[{"award-number":["BB\/N00521X\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>TreeGrafter is freely available on the web at https:\/\/github.com\/pantherdb\/TreeGrafter, including as a Docker image.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty625","type":"journal-article","created":{"date-parts":[[2018,7,19]],"date-time":"2018-07-19T22:46:32Z","timestamp":1532040392000},"page":"518-520","source":"Crossref","is-referenced-by-count":58,"title":["TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations"],"prefix":"10.1093","volume":"35","author":[{"given":"Haiming","family":"Tang","sequence":"first","affiliation":[{"name":"Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA"}]},{"given":"Robert D","family":"Finn","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Paul D","family":"Thomas","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,7,19]]},"reference":[{"key":"2023013107244624700_bty625-B1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"2023013107244624700_bty625-B2","doi-asserted-by":"crossref","first-page":"bar068","DOI":"10.1093\/database\/bar068","article-title":"Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation","volume":"2012","author":"Burge","year":"2012","journal-title":"Database (Oxford)"},{"key":"2023013107244624700_bty625-B3","doi-asserted-by":"crossref","first-page":"3674","DOI":"10.1093\/bioinformatics\/bti610","article-title":"Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research","volume":"21","author":"Conesa","year":"2005","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023013107244624700_bty625-B4","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1093\/bib\/bbr042","article-title":"Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium","volume":"12","author":"Gaudet","year":"2011","journal-title":"Brief. Bioinformatics"},{"key":"2023013107244624700_bty625-B5","doi-asserted-by":"crossref","first-page":"D183","DOI":"10.1093\/nar\/gkw1138","article-title":"PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements","volume":"45","author":"Mi","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2023013107244624700_bty625-B6","doi-asserted-by":"crossref","first-page":"D213","DOI":"10.1093\/nar\/gku1243","article-title":"The InterPro protein families database: the classification resource after 15 years","volume":"43","author":"Mitchell","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023013107244624700_bty625-B7","first-page":"1312","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023013107244624700_bty625-B8","doi-asserted-by":"crossref","first-page":"D331","DOI":"10.1093\/nar\/gkw1108","article-title":"Expansion of the Gene Ontology knowledgebase and resources","volume":"45","author":"The Gene Ontology Consortium","year":"2017","journal-title":"Nucleic Acids Research"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/3\/518\/48965471\/bioinformatics_35_3_518.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/3\/518\/48965471\/bioinformatics_35_3_518.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T10:18:19Z","timestamp":1675160299000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/3\/518\/5056037"}},"subtitle":[],"editor":[{"given":"Russell","family":"Schwartz","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,7,19]]},"references-count":8,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2019,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty625","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,2,1]]},"published":{"date-parts":[[2018,7,19]]}}}