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 Sequence containing the DNA sequence taken from the field “ORIGIN” in GenBank. The sequence is a vector of single characters.

Locus or accession

The returned list has a component Locus/Accession containing the names of the locus or accession number taken from the field “LOCUS” or “ACCESSION” in GenBank.

Species

The returned list has an attribute Species containing the names of the species taken from the field “ORGANISM” in GenBank.

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

[Package seq2R version 2.0.1 Index]