seqinr (version 1.0-3)

choosebank: To select a database structured under ACNUC and located on the web

Description

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 references.

Usage

choosebank(bank = NA, host = "pbil.univ-lyon1.fr", port = 5558, verbose = FALSE,
              timeout = 5, infobank = FALSE, tagbank = NA)

Arguments

bank

String. The name of the bank. If NA, choosebank will return the names of all database known by the server.

host

String. Host name for port

port

Integer. The TCP port number

verbose

Logical. If TRUE, verbose mode is on

timeout

Integer. The timeout in seconds for socketConnection. Default 5 seconds.

infobank

Logical. If infobank is TRUE and bank is NA, a data.frame with all database informations will be returned

tagbank

String. If bank is NA and tagbank is documented, the names of special purposes databases are returned. Current allowed values are TP for frozen databases and TEST for test database

Value

• When called with a regular bank name, an (invisible) list with five components
• [object Object],[object Object],[object Object],[object Object],[object Object]
• When called with bank = NA
• [object Object]
• When called with bank = NA and infobank = TRUE, a data.frame with three columns
• [object Object],[object Object],[object Object]

Details

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.

References

For more information about the socket communication protocol with ACNUC please get at http://pbil.univ-lyon1.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://pbil.univ-lyon1.fr/search/releases.php 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. To have an overview of the seqinR's functionnality, please consult this vignette: Charif, D., Lobry, J.R. (2005) SeqinR: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. Springer Verlag, Biological and Medical Physics/Biomedical Series, in press.

See Also

query, connection, socketConnection

Examples

mybank <- choosebank()
  choosebank(mybank[1])