BoSSA (version 1.2)

TaxoGB: Search for taxonomy information in genbank from a text query

Description

This function used the ESearch and ESpell tool from Eutils (http://eutils.ncbi.nlm.nih.gov/) to obtain taxonomy information from a text query. In case no hit is obtain, a mispell search is done.

Usage

TaxoGB(X,tsleep=3,organism="viridiplantae")

Arguments

X

a vector of accession numbers

tsleep

the time between two query to genbank. set to 3 (the unit is the second) as asked by GenBank

organism

a GenBank search query on organism. set to "viridiplantae" by default. See http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml for details

Value

The output is a character string with value tab separated. It includes the query, the taxonomy ID from GenBank, the Family, species and subspecies and a proposition of correction in case of possible mispell.

Details

Require the R4X package (available at http://r-forge.r-project.org/projects/r4x/) and internet connexion.

See Also

read.GenBank

Examples

#require internet connexion
#require R4X package, available at http://r-forge.r-project.org/projects/r4x/
#TaxoGB("tomato")
#TaxoGB("tomata")