R: Read DNA Sequences from GenBank via Internet

read.GenBank {ape} | R Documentation

## Read DNA Sequences from GenBank via Internet

### Description

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

### 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` | obsolete (will be removed soon).
`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 retrieved.

If `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 The option `gene.names` is obsolete and will be removed; this information is also present in the description.

Setting `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).

### Value

A list of DNA sequences made of vectors of class `"DNAbin"`, or of single characters (if `as.character = TRUE`) with two attributes (species and description).

### Author(s)

Emmanuel Paradis

### See Also

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

### 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.
    ## 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]]
    ## the description from each FASTA sequence:
    attr(Rampho, "description")

    ## End(Not run)

[Package ape version 5.1 Index]