choosebank              package:seqinr              R Documentation

_T_o _s_e_l_e_c_t _a _d_a_t_a_b_a_s_e _s_t_r_u_c_t_u_r_e_d _u_n_d_e_r _A_C_N_U_C _a_n_d _l_o_c_a_t_e_d _o_n _t_h_e _w_e_b

_D_e_s_c_r_i_p_t_i_o_n:

     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'.

_U_s_a_g_e:

     choosebank(bank = NA, host = "pbil.univ-lyon1.fr", port = 5558))

_A_r_g_u_m_e_n_t_s:

    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

_D_e_t_a_i_l_s:

     '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.

_V_a_l_u_e:

     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 

_N_o_t_e:

     The object of class 'socket' will be the first argument of the
     'query' function.

_A_u_t_h_o_r(_s):

     D. Charif

_R_e_f_e_r_e_n_c_e_s:

     For further information about socket, please see 'connection'
     function. For more information about the socket communication
     protocol with ACNUC please get at <URL:
     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: <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. 

_S_e_e _A_l_s_o:

     'query', 'connection'

_E_x_a_m_p_l_e_s:

       ## Not run:  mybank = choosebank() 
       ## Not run:  choosebank(mybank[1]) 

