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:
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