get_selfhyb_subseq {microRNA} | R Documentation |
This function finds the longest self-hybridizing subsequences present in RNA or DNA sequences.
get_selfhyb_subseq(seq, minlen, type = c("RNA", "DNA")) show_selfhyb_counts(L) show_selfhyb_lengths(L)
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
|
type |
one of |
L |
The output of |
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.
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. |
Seth Falcon
if (suppressWarnings(require(Rlibstree, quietly=TRUE))) { 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) }