spider (version 1.1-0)

read.BOLD: Downloads DNA sequences from the Barcode of Life Database (BOLD)

Description

These functions allow DNA sequences to be downloaded from the Barcode of Life Database (BOLD).

Usage

search.BOLD(taxon)
read.BOLD(IDs)

Arguments

taxon

A character vector of the names of the taxa of interest.

IDs

A character vector containing BOLD process ID numbers.

Value

• search.BOLD returns a character vector giving the process identification numbers of the specimens found by the search.

  read.BOLD returns an object of class `DNAbin'. This object has the attributes "species", "accession_num", and "gene".

Warning

On 26 Oct 2011, attempts to access records using the eFetch system through a web browser resulted in an error, saying that eFetch and eSearch are offline for maintainance. To test if these services are running, check the following URL in a web browser:

http://services.boldsystems.org/eFetch.php?record_type=specimen&id_type=sampleid&ids=DQ116162&return_type=xml

Details

search.BOLD retrieves BOLD process identification numbers for any given taxon using BOLD's eSearch system.

read.BOLD downloads the sequences associated with the process identification numbers using the eFetch web service offered by BOLD to enable batch retrieval of records.

References

BOLD web services: http://services.boldsystems.org/.

See Also

read.GB.

Examples

nn <- search.BOLD("Pisauridae")
pisaurid <- read.BOLD(nn)

write.dna(pisaurid, "filename.fas", format="fasta")