AAAlignment-class         package:pairseqsim         R Documentation

"_A_A_A_l_i_g_n_m_e_n_t" _r_e_s_u_l_t _o_f _p_a_i_r_w_i_s_e _s_e_q_u_e_n_c_e _a_l_i_g_n_m_e_n_t.

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

     Result of a pairwise sequence alignment.

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

     Objects can be created by calls of the form 'new("AAAlignment",
     ...)'.

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

     '_i_n_f_o_1': Object of class '"character"' :  name of first sequence. 

     '_i_n_f_o_2': Object of class '"character"' : name of second sequence 

     '_s_e_l_f_s_1': Object of class '"numeric"' : selfscore of sequence 1 

     '_s_e_l_f_s_2': Object of class '"numeric"' : selfscore of sequence 2

     '_s_c_o_r_e': Object of class '"numeric"' : Smith Watermann score of
          alignment. 

     '_i_d_e_n_t_i_t_y': Object of class '"numeric"' : nr of identitacal AA in
          the alignment.

     '_a_l_i_g_n_s_i_m_i_l_a_r_i_t_y': Object of class '"numeric"' : nr of
          similarities.

     '_l_c_h_1': Object of class '"numeric"' : length of sequence 1.

     '_l_c_h_2': Object of class '"numeric"' : length of sequence 2 

     '_a_l_i_g_1': Object of class '"character"' : alignment string 

     '_a_l_i_g_2': Object of class '"character"' : alignment string 

     '_b_e_a_u_t_i_f_y': Object of class '"character"' : internal 

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

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

     _s_u_m_m_a_r_y 'signature(object = "AAAlignment")': summary 

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

     Witold E. Wolski

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

     'salign-methods'

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

     data(EBLOSUM62)
     seq1<-new("AASequence","MEDQVGFGFRPNDEEL",info="seq1")
     seq2<-AASequence("seq1","VAISEVNICSYDPWNL")
     res<-salign(seq1,seq2,EBLOSUM62,delta=-10,gapext=-1,alignment="global")
     class(res)
     summary(res)

