biomartr (version 0.0.1)

listDatabases: Retrieve a List of Available Databases for Download

Description

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

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")