Skip to contents

Retrieve a List of Available NCBI Databases for Download

Source: R/listDatabases.R, R/listNCBIDatabases.R
listDatabases.Rd

This function allows you to retrieve a list of database names and versions that can be downloaded from correspondning servers.

Database retrieval is crucial for most biological studies and analyses. There is a vast diversity of databases that can be accessed remotely or that can be downloaded to your local machine. This function provides an interface to databases that can be downloaded from NCBI servers and lists all available databases and their database version to be able to select an appropriate database for download with download.database.

Usage

listDatabases(db = "nr", update = FALSE)

listNCBIDatabases(db = "nr", update = FALSE)

Arguments

db

a character string specifying the name of the database that shall be searched for.

update

a logical value specifying whether or not the local listDatabases.txt file shall be updated by remote access to NCBI.

See also

download.database, download.database.all

Author

Hajk-Georg Drost

Examples

if (FALSE) { # \dontrun{
# retrieve all versions of the NCBI 'nr' database that can be downloaded
listNCBIDatabases(db = "nr")

# analogous:
# listNCBIDatabases(db = "cdd")
# listNCBIDatabases(db = "nt")
# listNCBIDatabases(db = "gss")
# listNCBIDatabases(db = "refseq_protein")
} # }