This function connects to the GenBank database, and reads nucleotide sequences using accession numbers given as arguments.
a vector of mode character giving the accession numbers.
the names to give to each sequence; by default the accession numbers are used.
a logical indicating whether to attribute the species names to the returned object.
obsolete (will be removed soon).
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 retrieved.
species.names = TRUE, the returned list has an attribute
"species" containing the names of the species taken from the
field “ORGANISM” in GenBank.
Since ape 3.6, this function retrieves the sequences in FASTA format:
this is more efficient and more flexible (scaffolds and contigs can be
read). The option
gene.names is obsolete and will be removed;
this information is also present in the description.
species.names = FALSE is quite faster (could be useful
if you read a series of scaffolds or contigs, or if you already have
the species names).
A list of DNA sequences made of vectors of class
of single characters (if
as.character = TRUE) with two
attributes (species and description).
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## 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[] ## the description from each FASTA sequence: attr(Rampho, "description") ## End(Not run)
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