This function connects to the GenBank database, and reads nucleotide sequences using locus code given as arguments.
read.genbank(locus)
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.
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.
The returned list has an attribute Species containing the names of the species taken from the field ``ORGANISM'' in GenBank.
Vector of mode character giving the locus code or accession number.
Nora M. Villanueva and Marta Sestelo.
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.
Bethesda M. D. (2010) Entrez Programming Utilities Help. NCBI Help Manual. NCBI, USA
library(seq2R)
#mthumanDNA <- read.genbank("NC_012920")
#mthumanDNA
Run the code above in your browser using DataLab