bold_identify {bold}R Documentation

Search for matches to sequences against the BOLD COI database.


Search for matches to sequences against the BOLD COI database.


bold_identify(sequences, db = "COX1", response = FALSE, ...)



(character) Returns all records containing matching marker codes. Required. One or more. See Details.


(character) The database to match against, one of COX1, COX1_SPECIES, COX1_SPECIES_PUBLIC, OR COX1_L604bp. See Details for more information.


(logical) Note that response is the object that returns from the Curl call, useful for debugging, and getting detailed info on the API call.


Further args passed on to crul::verb-GET, main purpose being curl debugging

BOLD only allows one sequence per query. We internally lapply over the input values given to the sequences' parameter to search with one sequence per query. Remember this if you have a lot of sequences - you are doing a separate query for each one, so it can take a long time - if you run into errors let us know.


A data.frame with details for each specimen matched. if a failed request, returns NULL

db parmeter options

Named outputs

To maintain names on the output list of data make sure to pass in a named list to the sequences parameter. You can for example, take a list of sequences, and use stats::setNames() to set names.


See Also



## Not run: 
seq <- sequences$seq1
res <- bold_identify(sequences=seq)
head(bold_identify(sequences=seq, db='COX1_SPECIES')[[1]])

## End(Not run)

[Package bold version 1.2.0 Index]