biomartr (version 0.1.0)

listDatabases: Retrieve a List of Available NCBI Databases for Download

Description

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_name = "nr", db_format = "fasta", update = FALSE)

Arguments

db_name

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

db_format

a character string specifying the database format, e.g. db_format = "fasta".

update

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

References

ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA

See Also

download_database

Examples

# retrieve all versions of the NCBI 'nr' database that can be downloaded
# listDatabases(db_name = "nr", db_format = "fasta")

# analogous:
# listDatabases(db_name = "cdd", db_format = "fasta")
# listDatabases(db_name = "nt", db_format = "fasta")
# listDatabases(db_name = "gss", db_format = "fasta")
# listDatabases(db_name = "refseq_protein", db_format = "fasta")