read.GenBank: Read DNA Sequences from GenBank via Internet
In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description Usage Arguments Details Value Author(s) See Also Examples

This function connects to the GenBank database, and reads nucleotide sequences using accession numbers given as arguments.

1 2	read.GenBank(access.nb, seq.names = access.nb, species.names = TRUE, gene.names = FALSE, as.character = FALSE)

`access.nb`	a vector of mode character giving the accession numbers.
`seq.names`	the names to give to each sequence; by default the accession numbers are used.
`species.names`	a logical indicating whether to attribute the species names to the returned object.
`gene.names`	a logical indicating whether to attribute the gene names to the returned object. It is `FALSE` by default because this will work correctly only when reading sequences with a single gene.
`as.character`	a logical controlling whether to return the sequences as an object of class `"DNAbin"` (the default).

The function uses the site http://www.ncbi.nlm.nih.gov/ from where the sequences are downloaded.

If species.names = TRUE, the returned list has an attribute "species" containing the names of the species taken from the field “ORGANISM” in GenBank.

If gene.names = TRUE, the returned list has an attribute "gene" containing the names of the gene. This will not work correctly if reading a sequence with multiple genes (e.g., a mitochondrial genome).

A list of DNA sequences made of vectors of class "DNAbin", or of single characters (if as.character = "TRUE").

Emmanuel Paradis

read.dna, write.dna, dist.dna, DNAbin

### This won't work if your computer is not connected
### to the Internet!!!
###
### Get the 8 sequences of tanagers (Ramphocelus)
### as used in Paradis (1997)
ref <- c("U15717", "U15718", "U15719", "U15720",
         "U15721", "U15722", "U15723", "U15724")
### Copy/paste or type the following commands if you
### want to try them.
## Not run: 
Rampho <- read.GenBank(ref)
### get the species names:
attr(Rampho, "species")
### build a matrix with the species names and the accession numbers:
cbind(attr(Rampho, "species"), names(Rampho))
### print the first sequence
### (can be done with `Rampho$U15717' as well)
Rampho[[1]]
### print the first sequence in a cleaner way
cat(Rampho[[1]], "\n", sep = "")

## End(Not run)