get_selfhyb_subseq         package:microRNA         R Documentation

_G_e_t _S_e_l_f-_H_y_b_r_i_d_i_z_i_n_g _S_u_b_s_e_q_u_e_n_c_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function finds the longest self-hybridizing subsequences
     present in RNA or DNA sequences.

_U_s_a_g_e:

     get_selfhyb_subseq(seq, minlen, type = c("RNA", "DNA"))
     show_selfhyb_counts(L)
     show_selfhyb_lengths(L)

_A_r_g_u_m_e_n_t_s:

     seq: character vector of RNA or DNA sequences

  minlen: an integer specifying the minimum length in bases of the
          self-hybridizing subsequences.  Subsequences with length less
          than 'minlen' will be ignored.

    type: one of '"RNA"' or '"DNA"' depending on the type of sequences
          provided in 'seq'.  Note that you cannot mix RNA and DNA
          sequences.

       L: The output of 'get_selfhyp_subseq'.

_D_e_t_a_i_l_s:

     'get_selfhyb_subseq' finds the longest self-hybridizing
     subsequences of the specified minimum length.  It does this using
     suffix trees and the 'getLongestSubstring' function provided by
     the Rlibstree package.

     These are defined to be the longest string that is found in both
     the input sequence, 'seq', and in its reverse complement.

_V_a_l_u_e:

     A list with an element for each sequence in 'seq'.  The list will
     be named using 'names(seq)'.

     Each element is itself a list with an element for each longest
     self-hybridizing subsequence (there can be more than one).  Each
     such element is yet another list with components:

  starts: integer vector giving the character start positions for the
          self-hybridizing subsequence in the sequence.

rcstarts: integer vector giving the character start positions for the
          reverse complement of the self-hybridizing subsequence in the
          sequence.

_A_u_t_h_o_r(_s):

     Seth Falcon

_E_x_a_m_p_l_e_s:

     seqs = c(a="UGAGGUAGUAGGUUGUAUAGUU", b="UGAGGUAGUAGGUUGUGUGGUU",
              c="UGAGGUAGUAGGUUGUAUGGUU")

     ans = get_selfhyb_subseq(seqs, minlen=3, type="RNA")
     length(ans)

     ans[["a"]]

     show_selfhyb_counts(ans)
     show_selfhyb_lengths(ans)

