ncbiGenome: NCBI Genome links to the Nucleotide database

In cstubben/genomes2: Genome sequencing project metadata

Description

Search Entrez Genome at NCBI and retrieves linked genomes in the Nucleotide database

Usage

ncbiGenome(term, refseq=FALSE)

Arguments

term	Any valid combination of Entrez search terms
refseq	Include RefSeq genomes, default is GenBank submissions

Details

Searches Entrez Genome and finds linked sequences in Entrez Nucleotide using genome_nuccore (Assembly) and then finds related sequences using nuccore_nuccore_samespecies_rsgb (Other INSDC Genome Sequences). The genome_nuccore link includes the Reference and Genbank acc that Reference was derived from (and refseq option is used to exclude duplicate RefSeq from results).

Value

A genomes data frame with acc, name, created, taxid, size, gi and other fields.

Author(s)

Chris Stubben

References

A description of the Entrez programming utilities is at http://eutils.ncbi.nlm.nih.gov/.

Examples

## Not run: 
ncbiGenome('Nipah virus[orgn]')
ncbiGenome('Nipah virus[orgn]', refseq=TRUE)

## End(Not run)

cstubben/genomes2 documentation built on May 14, 2019, 12:25 p.m.