read.GenBank {ape} | R Documentation |
This function connects to the GenBank database, and reads nucleotide sequences using accession numbers given as arguments.
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 |
as.character |
a logical controlling whether to return the
sequences as an object of class |
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)