This function allows to select one of the databases structured under ACNUC and located on the web.
Called without arguments,
choosebank(), will return the list of available databases.
Then, you can use
query to make your query and get a list of sequence names.
Remote access to ACNUC databases works by opening a socket connection on a port (for example
on port number 5558 at pbil.univ-lyon1.fr) and by communicating on this socket following the protocol
described in the section
choosebank(bank = NA, host = "pbil.univ-lyon1.fr", port = 5558, server = FALSE, blocking = TRUE, open = "a+", encoding = "", verbose = FALSE, timeout = 5, infobank = FALSE, tagbank = NA)
When called with a regular bank name, an (invisible) list with 6 components:
an object of class
the name of the bank
the type of the bank (GENBANK, EMBL, SWISSPROT, NBRF)
the total number of sequences present in the opened database
the total number of species present in the opened database
the total number of keywords present in the opened database
When called with bank = NA:
A vector of all available bank names.
When called with bank = NA and infobank = TRUE, a data.frame with three columns:
The name of the bank.
The bank status (on/of).
Short description of bank with last release date.
string. The name of the bank. If NA,
choosebank will return the names of all database known by the server.
string. Host name for port (see
integer. The TCP port number (see
logical. Should the socket be a client or a server? (see
string. A description of how to open the connection (see
string. The name of the encoding to be used. (see
logical. If TRUE, verbose mode is on
integer. The timeout in seconds for
socketConnection. Default 5 seconds.
infobank is TRUE and
NA, a data.frame
with all database informations will be returned
tagbank is documented, the names
of special purposes databases are returned. Current allowed values are TP
for frozen databases (TP is an acronym for "travaux pratiques" which means practicals
in french, these databases are useful mainly for teaching so as to have stable results),
TEST for test databases, and DEV for databases under development (unstable).
D. Charif, J.R. Lobry
When called without arguments,
choosebank() returns a list of all the databases names known
by the server, as a vector of string. When called with
choosebank(infobank = TRUE), a data.frame
with more information is returned.
For more information about the socket communication protocol with ACNUC please get at http://doua.prabi.fr/databases/acnuc/remote_acnuc.html.
To get the release date and content of all the databases located at the pbil, please look at the following url: http://doua.prabi.fr/search/releases
Gouy, M., Milleret, F., Mugnier, C., Jacobzone, M., Gautier,C. (1984) ACNUC: a nucleic acid sequence data base and analysis system. Nucl. Acids Res., 12:121-127.
Gouy, M., Gautier, C., Attimonelli, M., Lanave, C., Di Paola, G. (1985) ACNUC - a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage. Comput. Appl. Biosci., 3:167-172.
Gouy, M., Gautier, C., Milleret, F. (1985) System analysis and nucleic acid sequence banks. Biochimie, 67:433-436.
if (FALSE) # Need internet connection # Show available databases: choosebank() # Show frozen databases: choosebank(tag = "TP") # Select a database: choosebank("emblTP", tag = "TP") # Do something with the database: myseq <- gfrag("LMFLCHR36", start = 1, length = 30) stopifnot(myseq == "cgcgtgctggcggcaatgaagcgttcgatg") # Close the database: closebank()
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