MSBind

The MSbind tool calculates features of meta-stable RNA secondary structure target sites. MSbind accepts as input a file containing RNA secondary structures in dot bracket notation such as that output by the barrier tool from the Vienna RNA package.

This tool was used to analyse the accessibility of microRNA binding sites in metastable RNA secondary structures in the presence of SNPs.

MSbind:

  • Sorts meta-stable structures by number of base pairings within the target site.
  • Approximates the opening energies of meta-stable target sites using RNAeval.
  • Averages the opening energy and depth of meta-stable structures.
Input Flags:

-f : MSbind accepts as input a file of RNA secondary structures in dot bracket notation as produced by the barrier tool from the Vienna RNA package

-s : Target start position

-e : Target out position

-o : Output file

-c : (Optional) Number of local minima to read from input file

Usage Example:

./MSbind -f infile -s 224 -e 232 -o outfile -c 100

About

Version
1.0
Released
01/01/2013
Author(s)
Luke Day
Dependencies
Vienna RNA Package

Downloads

MSBind
Download Perl Script
RNAsubopt & Barrier Filter
Download Perl Script
Both Scripts & Vienna RNA Package 2.0
Download Tar Archive