DNAPatternAlphabet        package:Biostrings        R Documentation

_f_u_n_c_t_i_o_n_s _t_o _c_r_e_a_t_e _D_N_A _a_n_d _R_N_A _p_a_t_t_e_r_n _a_l_p_h_a_b_e_t_s

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

     The function 'DNAAlphabet' returns an alphabet consisting of
     standard patterns used in DNA sequences.

     The function 'RNAAlphabet' returns an alphabet consisting of
     standard patterns used in RNA sequences.

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

     DNAPatternAlphabet()
     RNAPatternAlphabet()

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

     An object of class "BioPatternAlphabet". See
     'BioPatternAlphabet-class' for details.

_M_e_m_e_b_e_r_s _o_f _t_h_e _p_a_t_t_e_r_n _a_l_p_h_a_b_e_t_s:

     In the table below, we provide the letters from the base DNA
     alphabet that are matched by the added letters in the DNA pattern
     alphabet. The corresponding table for RNA is identical except for
     the substitution of 'U' for 'T'.

       'N'  matches 'A', 'C', 'G', 'T'
       'B'  matches 'C', 'G', 'T'
       'D'  matches 'A', 'G', 'T'
       'H'  matches 'A', 'C', 'T'
       'K'  matches 'G', 'T'
       'M'  matches 'A', 'C'
       'R'  matches 'A', 'G'
       'S'  matches 'C', 'G'
       'V'  matches 'A', 'C', 'G'
       'W'  matches 'A', 'T'
       'Y'  matches 'C', 'T'
            

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

     Saikat DebRoy

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

     'DNAAlphabet', 'RNAAlphabet'

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

     DNAPatternAlphabet()
     RNAPatternAlphabet()

