salign-methods          package:pairseqsim          R Documentation

_O_p_t_i_m_a_l _p_a_i_r_w_i_s_e _a_l_i_g_n_m_e_n_t _o_f _t_w_o _p_r_o_t_e_i_n _s_e_q_u_e_n_c_e_s.

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

     Computes optimal pairwise alignment of 2 protein sequences.

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

    obj1: see above

    obj2: see above

     sub: Substitution matrix

   delta: gap opening penalty

  gapext: gap extension penalty

alignment: type of alignment: c("global","local","overlap")

 scoring: type of scoring, identity, similarity, score, scoreN,
          AAAlignemnt, pozitive

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

     For two objects of class 'AASequence' returns an object of class
     'AAAlignment'.  Otherwise it returns a score. If used with 'NULL'
     as second parameter it returns a distance matrix. The scores than
     are transformed into distances. For details see the vignette.

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

     _o_b_j_1 = "_A_A_S_e_q_u_e_n_c_e_L_i_s_t", _o_b_j_2 = "_N_U_L_L" Compute distance matrix.

     _o_b_j_1 = "_A_A_S_e_q_u_e_n_c_e_L_i_s_t", _o_b_j_2 = "_A_A_S_e_q_u_e_n_c_e" Compute scores.

     _o_b_j_1 = "_A_A_S_e_q_u_e_n_c_e", _o_b_j_2 = "_A_A_S_e_q_u_e_n_c_e_L_i_s_t" Compute scores.

     _o_b_j_1 = "_A_A_S_e_q_u_e_n_c_e", _o_b_j_2 = "_A_A_S_e_q_u_e_n_c_e" Compute alignment.

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

     Witold E. Wolski

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

     Hilary S Booth, John H Maindonald, Ole M Nielsen, Susan R Wilson
     "Normalizing sequence alignment scores for composition bias"
     Recomb 2003 - Berlin

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

     data(sequlist)
     data(EPAM110)
     #example of alignment
     res<-salign(sequlist[[1]],sequlist[[2]],EPAM110,delta=-4,gapext=-1,alignment="global")
     summary(res)
     #scoring a sequence against a list of sequences.
     res <- salign( sequlist[1:10] , sequlist[[1]], EPAM110 , delta = -4,gapext = -1,alignment = "local", scoring = "score")
     hist(res)
     #computing a distance matrix.
     res<-salign(sequlist[1:10],NULL,EPAM110,delta=-10,gapext=-1,alignment="overlap",scoring="pozitive")
     hist(as.numeric(res))

