testalign-methods         package:pairseqsim         R Documentation

_S_c_o_r_i_n_g _o_f _o_p_t_i_m_a_l _a_l_i_n_g_m_e_n_t_s.

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

     Computes optimal pairwise alignment of 2 protein sequences. For
     internal use.

_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,
          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 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", _o_b_j_2 = "_A_A_S_e_q_u_e_n_c_e" Computes obtimal
          alignment of two sequences and returns score.

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

     Witold E. Wolski

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

     <URL: http://r4proteomics.sourceforge.net>

