PANTHER Tree Grafter

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 50,000 characters.

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.

Value

A list containing PANTHER tree topology information.

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, doi:10.1093/bioinformatics/bty625

Corresponding API Resources

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

References

• Thomas PD, Ebert D, Muruganujan A, Mushayahama T, Albou L-P, Mi H. (2022) PANTHER: Making genome-scale phylogenetics accessible to all. Protein Science, 31(1), 8–22. https://doi.org/10.1002/pro.4218

• PANTHER Services Details

• Citations note on PANTHER website

See also

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

Examples

# \donttest{
rba_panther_tree_grafter("MKVLWAALLVTFLAGCQAKVEQAVETE")
# }