Submatrix-class          package:pairseqsim          R Documentation

_C_l_a_s_s "_S_u_b_m_a_t_r_i_x" _S_u_b_s_t_i_t_u_t_i_o_n _M_a_t_r_i_x

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

     Amino Acid Substitution Matrices

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     'new("Submatrix", ...)'. or 'data(EPAM100'

_S_l_o_t_s:

     '._D_a_t_a': Object of class '"matrix"' substitution matrix 

     '_c_o_p_y_r_i_g_h_t': Object of class '"character"' GNU GPL2 

     '_i_n_f_o': Object of class '"character"' name

     '_h_e_a_d': Object of class '"character"' description

     '_a_l_p_h_a_b_e_t': Object of class '"character"' alphabet

_E_x_t_e_n_d_s:

     Class '"matrix"', directly.

_M_e_t_h_o_d_s:

     _s_e_l_f_a_l_i_g_n 'signature(object = "AASequence", sub = "Submatrix")':
          compute teh score for aligning the sequence with itself 

     _s_h_o_w 'signature(object = "Submatrix")': show

     _s_u_b_F_r_o_m_E_m_b_o_s_s 'signature(object = "Submatrix", path =
          "character")': read Substitution matrices from EMBOSS package 

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

     Witold Eryk Wolski

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

     http://www.hgmp.mrc.ac.uk/Software/EMBOSS/overview.html

