read.genbank {seq2R} | R Documentation |
Read DNA sequences from GenBank via internet
Description
This function connects to the GenBank database, and reads nucleotide sequences using locus code given as arguments.
Usage
read.genbank(locus)
Arguments
locus |
Vector of mode character giving the locus code or accession number. |
Details
This function uses the site https://pubmed.ncbi.nlm.nih.gov/ (E-utilities) from where the sequences are downloaded. E-utilities are a set of eight server-side programs that provide a stable interface into the Entrez query and database system at the National Center for Biotechnology Informatio (NCBI). The E-utilities use a fixed URL syntax that translates a standard set of input parameters into the values necessary for various NCBI software components to search for and retrieve the requested data. The E-utilities are therefore the structured interface to the Entrez system, which currently includes 38 databases covering a variety of biomedical data, including nucleotide and protein sequences, gene records, three-dimensional molecular structures, and the biomedical literature.
Value
Sequence |
The returned list has a component |
Locus or accession |
The returned list has a component |
Species |
The returned list has an attribute |
Note
If the computer is not connected to the internet, this function will not work.
Author(s)
Nora M. Villanueva and Marta Sestelo.
References
Bethesda M. D. (2010) Entrez Programming Utilities Help. NCBI Help Manual. NCBI, USA
Examples
library(seq2R)
#mthumanDNA <- read.genbank("NC_012920")
#mthumanDNA