rba_panther_tree_grafter: PANTHER Tree Grafter

In rbioapi: User-Friendly R Interface to Biologic Web Services' API

PANTHER Tree Grafter

Description

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.

Usage

rba_panther_tree_grafter(protein_seq, target_organisms = NULL, ...)

Arguments

protein_seq	A character string with the protein's sequence. Maximum allowed sequence length is 50kb.
target_organisms	(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.

Details

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, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/bty625")}

Value

A list containing PANTHER tree topology information.

Corresponding API Resources

"GET https://www.pantherdb.org/services/oai/pantherdb/graftsequence"

References

• 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

• PANTHER Services Details

• Citations note on PANTHER website

See Also

Other "PANTHER": rba_panther_enrich(), rba_panther_family(), rba_panther_homolog(), rba_panther_info(), rba_panther_mapping(), rba_panther_ortholog()

Examples

rba_panther_tree_grafter("MKVLWAALLVTFLAGCQAKVEQAVETE")

rbioapi documentation built on April 4, 2025, 5:04 a.m.