PFAMSCOP               package:PFAM.db               R Documentation

_M_a_p_p_i_n_g_s _f_r_o_m _a _P_F_A_M _A_c_c_e_s_s_i_o_n _n_u_m_b_e_r _t_o _a _S_C_O_P _I_D

_D_e_s_c_r_i_p_t_i_o_n:

     This is an R object that always contains mappings from a PFAM
     accession (AC) to a SCOP ID

_D_e_t_a_i_l_s:

     The SCOP ID along with the start point and end point have been
     attached to the PFAM accessions in this object.

     More Details: Structural Classification of Proteins (<URL:
     http://scop.mrc-lmb.cam.ac.uk/scop/index.html>).  Reference:
     Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). SCOP:
     a structural classification of proteins database for the
     investigation of sequences and structures. J. Mol. Biol. 247,
     536-540

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.sanger.ac.uk/Software/Pfam/> and <URL:
     ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/userman.txt>

_E_x_a_m_p_l_e_s:

             #To map from PFAM to SCOP:
             x <- PFAMSCOP
             # Get the PFAM identifiers that are mapped to a SCOP
             mapped_keys <- mappedkeys(x)
             # Convert to a list
             xx <- as.list(x[mapped_keys])
             if(length(xx) > 0) {
               # Get the SCOP info for the first five PFAM IDs
               xx[1:5]
               # Get the first one
               xx[[1]]
             }

