Retrieve gene sequences from NCBI by accession number.
Arguments
- ids
(character) GenBank ids to search for. One or more. Required.
- format
(character) Return type, e.g.,
"fasta"
. NOW IGNORED.- verbose
(logical) If
TRUE
(default), informative messages printed.
Value
data.frame of the form:
taxon - taxonomic name (may include some junk, but hard to parse off)
taxonomy - organism lineage
gene_desc - gene description
organelle - if mitochondrial or chloroplast
gi_no - GI number
acc_no - accession number
keyword - if official DNA barcode
specimen_voucher - museum/lab accession number of vouchered material
lat_lon - longitude/latitude of specimen collection event
country - country/location of specimen collection event
paper_title - title of study
journal - journal study published in (if published)
first_author - first author of study
uploaded_date - date sequence was uploaded to GenBank
length - sequence length
sequence - sequence character string
Details
If bad ids are included with good ones, the bad ones are silently dropped. If all ids are bad you'll get a stop with error message.
See also
ncbi_searcher()
, ncbi_byname()]
Examples
if (FALSE) {
# A single gene
ncbi_byid(ids="360040093")
# Many genes (with different accession numbers)
ncbi_byid(ids=c("360040093","347448433"))
}