blast: use NCBI blast

Description

This function use the BLAST URL-API and query either DNA sequences store in object of class "DNAbin" or accession numbers

Usage

blast(X, program = "blastn", database = "nr", entrezquery = "none", nb = 5, oot = 35)

Arguments

either an object of class "DNAbin" or a vector of accession numbers

program

specify the BLAST program to use. either "blastn" (default), "blastp", "blastx", "tblastn", "tblastx"

database

specify the database to use. See the reference section

entrezquery

add an entrez query

maximal number of hit to display

oot

out of time parameter. Default correpsond to a maximum of 2 minutes search

Value

the output is a list where each compartment correspond to a blast search. If the query was a "DNAbin" object, there is as many compartment as sequence in the object. If the query was an accession numbers vector, there is as many compartment as accession numbers in the vector. Each blast result is a data.frame with the accession number of the hit, the definition of the hit (i.e. the name), the score and the evalue as colomns.

References

BLAST URL-API : http://www.ncbi.nlm.nih.gov/blast/Doc/urlapi.html

BLAST homepage : http://blast.ncbi.nlm.nih.gov/Blast.cgi

Entrez query : http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml

Examples

Run this code

#require internet connexion
#require R4X package, available at http://r-forge.r-project.org/projects/r4x/
#blast("aj865339")
#blast("aj865339",entrezquery="viridiplantae[organism]")