taxize (version 0.6.0)

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

Description

THIS FUNCTION IS DEFUNCT.

Usage

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

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.

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