Prediction of RNA-RNA interaction structure by centroids in the Boltzmann ensemble

Details Prediction of RNA-RNA interaction structure by centroids in the Boltzmann ensemble Prediction of RNA-RNA interaction structure by centroids in the Boltzmann ensemble

2010-02-08

arxiv.org/abs/1002.1736v1

Biology

Quantitative Biology

Biomolecules

Scientific paper

New high-throughput sequencing technologies have made it possible to pursue the advent of genome-wide transcriptomics. That progress combined with the recent discovery of regulatory non-coding RNAs (ncRNAs) has necessitated fast and accurate algorithms to predict RNA-RNA interaction probability and structure. Although there are algorithms to predict minimum free energy interaction secondary structure for two nucleic acids, little work has been done to exploit the information invested in the base pair probabilities to improve interaction structure prediction. In this paper, we present an algorithm to predict the Hamming centroid of the Boltzmann ensemble of interaction structures. We also present an efficient algorithm to sample interaction structures from the ensemble. Our sampling algorithm uses a balanced scheme for traversing indices which improves the running time of the Ding-Lawrence sampling algorithm. The Ding-Lawrence sampling algorithm has $O(n^2m^2)$ time complexity whereas our algorithm has $O((n+m)^2\log(n+m))$ time complexity, in which $n$ and $m$ are the lengths of input strands. We implemented our algorithm in a new version of {\tt piRNA} and compared our structure prediction results with competitors. Our centroid prediction outperforms competitor minimum-free-energy prediction algorithms on average.

Affiliated with

Also associated with

No associations

Rating

Prediction of RNA-RNA interaction structure by centroids in the Boltzmann ensemble does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with Prediction of RNA-RNA interaction structure by centroids in the Boltzmann ensemble, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Prediction of RNA-RNA interaction structure by centroids in the Boltzmann ensemble will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-123952