read.GenBank {ape}R Documentation

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)

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.

Details

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

Value

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

Author(s)

Emmanuel Paradis paradis@isem.univ-montp2.fr

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.
## Not run: 
Rampho <- read.GenBank(ref)
### 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)

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