ape (version 1.6)

read.GenBank: Read DNA Sequences from GenBank via Internet

Description

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

Usage

read.GenBank(access.nb, seq.names = access.nb,
             species.names = TRUE)

Arguments

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.

Value

• A list a DNA sequences each made of a single vector of mode character where each element is a nucleotide.

Details

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.

See Also

read.dna, write.dna, dist.dna

Examples

### This won't work if your computer is not connected
### to 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.
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 = "")