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)

