ncbi_byname: Retrieve gene sequences from NCBI by taxon name and gene...

In traits: Species Trait Data from Around the Web

Retrieve gene sequences from NCBI by taxon name and gene names.

Description

Retrieve gene sequences from NCBI by taxon name and gene names.

Usage

ncbi_byname(
  taxa,
  gene = "COI",
  seqrange = "1:3000",
  getrelated = FALSE,
  verbose = TRUE,
  batch_size = 100,
  ...
)

Arguments

taxa	(character) Scientific name to search for.
gene	(character) Gene or genes (in a vector) to search for. See examples.
seqrange	(character) Sequence range, as e.g., "1:1000". This is the range of sequence lengths to search for. So "1:1000" means search for sequences from 1 to 1000 characters in length.
getrelated	(logical) If TRUE, gets the longest sequences of a species in the same genus as the one searched for. If FALSE, returns nothing if no match found.
verbose	(logical) If TRUE (default), informative messages printed.
batch_size	An integer specifying the number of names to query per batch.
...	Curl options passed on to crul::verb-GET

Details

Removes predicted sequences so you don't have to remove them. Predicted sequences are those with accession numbers that have "XM_" or "XR_" prefixes. This function retrieves one sequences for each species, picking the longest available for the given gene.

Value

data.frame

Author(s)

Scott Chamberlain

See Also

ncbi_searcher(), ncbi_byid()

Examples

# Empty input returns immediately (no HTTP request)
ncbi_byname(taxa = character())


if (interactive()) {
  # A single species
  ncbi_byname(taxa = "Acipenser brevirostrum")

  # Many species
  species <- c("Colletes similis", "Halictus ligatus", "Perdita californica")
  ncbi_byname(taxa = species, gene = c("coi", "co1"), seqrange = "1:2000")
}

traits documentation built on April 10, 2026, 5:06 p.m.