seqinr (version 1.0-1)

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. Then, you can use query to compose your query and get a list of sequence names. Remote access to ACNUC databases work by opening a socket on a port (as an example on port number 5558 of 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))

Arguments

bank

The name of the bank. If NA, it returns the name of all database known by the server.

host

Host name for port

port

integer. The TCP port number

Value

• A list with five components
• socket
  an object of class socket
• bankname
  the name of the bank
• totseqs
  the total number of sequences present in the opened database
• totspecs
  the total number of species present in the opened database
• totkeys
  the total number of keywords present in the opened database

Details

choosebank() returns a list of all the databases located at the Pbil. See the reference section for more details. ACNUC databases are made of a series of flat text files (called divisions) containing annotations and sequences and a series of index files allowing efficient access to sequence data.

References

For further information about socket, please see connection function. 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 preparation.

See Also

query, connection

Examples

mybank = choosebank()
  choosebank(mybank[1])