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.
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
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)