needwunsQS            package:Biostrings            R Documentation

_q_u_a_d_r_a_t_i_c-_s_p_a_c_e, _s_i_m_p_l_e _g_a_p _i_m_p_l_e_m_e_n_t_a_t_i_o_n _o_f _N_e_e_d_l_e_m_a_n-_W_u_n_s_c_h
_g_l_o_b_a_l _a_l_i_g_n_m_e_n_t _a_l_g_o_r_i_t_h_m

_D_e_s_c_r_i_p_t_i_o_n:

     quadratic-space, simple gap implementation of Needleman-Wunsch
     global alignment algorithm

_U_s_a_g_e:

     needwunsQS(s1, s2, substmat, gappen=8)

_A_r_g_u_m_e_n_t_s:

      s1: s1: first string, an R character vector of length 1 or a
          BString instance

      s2: s2: second string, same data type as 's1'

substmat: substmat: matrix of alignment score values

  gappen: gappen: penalty for introducing a gap in the alignment

_D_e_t_a_i_l_s:

     follows specification of Durbin, Eddy, Krogh, Mitchison (1998).

_V_a_l_u_e:

     an instance of the S3 class ``needwunsQS'', for which there are
     print and alignScore methods.

_A_u_t_h_o_r(_s):

     Vince Carey <stvjc@channing.harvard.edu>

_R_e_f_e_r_e_n_c_e_s:

     R. Durbin, S. Eddy, A. Krogh, G. Mitchison,  Biological Sequence
     Analysis, Cambridge UP 1998, sec 2.3.

_E_x_a_m_p_l_e_s:

     data(blosum50)
     needwunsQS( "PAWHEAE", "HEAGAWGHEE", blosum50 )