get_selfhyb_subseq: Get Self-Hybridizing Subsequences

In microRNA: Data and functions for dealing with microRNAs

Description

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

Usage

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

Arguments

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.

Details

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.

Value

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.

Author(s)

Seth Falcon

Examples

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)

microRNA documentation built on Nov. 8, 2020, 7:50 p.m.