Use this function to retrieve a PANTHER family's tree topology information with a node corresponding to your sequence grafted in the best location in that tree.
rba_panther_tree_grafter(protein_seq, target_organisms = NULL, ...)A list containing PANTHER tree topology information.
A character string with the protein's sequence. Maximum allowed sequence length is 50kb.
(numeric) NCBI taxon ID(s) to filter the results.
run rba_panther_info with argument 'what = "organisms"' to
get a list of PANTHER's supported organisms.
rbioapi option(s). See rba_options's
arguments manual for more information on available options.
"GET https://www.pantherdb.org/services/oai/pantherdb/graftsequence"
For more information, see: Haiming Tang, Robert D Finn, Paul D Thomas, TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations, Bioinformatics, Volume 35, Issue 3, February 2019, Pages 518–520, tools:::Rd_expr_doi("10.1093/bioinformatics/bty625")
Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayamaha, Paul D Thomas, PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D394–D403, https://doi.org/10.1093/nar/gkaa1106
Other "PANTHER":
rba_panther_enrich(),
rba_panther_family(),
rba_panther_homolog(),
rba_panther_info(),
rba_panther_mapping(),
rba_panther_ortholog()
# \donttest{
rba_panther_tree_grafter("MKVLWAALLVTFLAGCQAKVEQAVETE")
# }
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