read.GenBank

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Read DNA Sequences from GenBank via Internet

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

Keywords
IO
Usage
read.GenBank(access.nb, seq.names = access.nb, species.names = TRUE,
             gene.names = FALSE, as.character = FALSE)
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.
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).
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.

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).

Value

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

See Also

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

Aliases
  • read.GenBank
Examples
### 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.
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 = "")
Documentation reproduced from package ape, version 2.7-3, License: GPL (>= 2)

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