RNAbound

Self-contained structured domains of RNA sequences have often distinct molecular functions. The RNAbound program helps to predict the boundaries of self-contained structured domain from the base pairing probability (P) matrix for a given sequence or multiple sequence alignment. The input matrix (P) can be computed using RNAfold for single sequence or PETfold for multiple sequence alignments.

Download

Software:RNAbound v1.0
Dataset: benchmark dataset

Usage

RNAbound program can be executed in two modes:

"rnabound.pl" : takes base pairing probability matrix (computed using RNAfold or PETfold) as input and predicts the boundaries
"run_bppCal_rnabound.sh" : takes single sequence or multiple sequence alignment as input, computes base pairing probability matrix (using RNAfold or PETfold) and then predicts the boundaries.

To run "run_bppCal_rnabound.sh", RNAfold and PETfold programs have to be installed locally and their corresponding path has to be specified in this script.

Dependencies

For more details about the execution and input format, please refer to the README file inside the package.

Publications

Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures

Sabarinathan R, Anthon C, Gorodkin J, Seemann SE* Genes (Basel). 2018 Dec 4;9(12):604
[ PubMed | Paper | Software ]

Contact

If you have any queries, please contact sabari@rth.dk or seemann@rth.dk