Get Self-Hybridizing Subsequences

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

Details

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.

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:

Author(s)

Seth Falcon

Examples

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)
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(microRNA)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/microRNA/get_selfhyb_subseq.Rd_%03d_medium.png", width=480, height=480)
> ### Name: get_selfhyb_subseq
> ### Title: Get Self-Hybridizing Subsequences
> ### Aliases: get_selfhyb_subseq show_selfhyb_counts show_selfhyb_lengths
> ### Keywords: manip
> 
> ### ** Examples
> 
> 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)
+ }
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>