taxize (version 0.2.0)

ncbi_getbyname: 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_getbyname(taxa, gene = "COI", seqrange = "1:3000",
  getrelated = FALSE, verbose = TRUE)

Arguments

taxa

Scientific name to search for (character).

gene

Gene (character) or genes (character vector) to search for.

seqrange

Sequence range, as e.g., "1:1000" (character).

getrelated

Logical, if TRUE, gets the longest sequences of a species in the same genus as the one searched for. If FALSE, get's nothing.

verbose

logical; If TRUE (default), informative messages printed.

Value

• Data.frame of results.

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.

See Also

ncbi_search, ncbi_getbyid

Examples

# A single species
ncbi_getbyname(taxa="Acipenser brevirostrum")

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