A Sampling Approach for Multiple RNA Interaction - Finding Sub-optimal Solutions Fast

Saad Mneimneh, Syed Ali Ahmed

2016

Abstract

The interaction of two RNA molecules involves a complex interplay between folding and binding that warranted recent developments in RNA-RNA interaction algorithms. These algorithms cannot be used to predict interaction structures when the number of RNAs is more than two. Our recent formulation of the multiple RNA interaction problem is based on a combinatorial optimization called Pegs and Rubber Bands, and has been successful in predicting structures that involve more than two RNAs. Even then, however, the optimal solution obtained does not necessarily correspond to the actual biological structure. Moreover, a structure produced by interacting RNAs may not be unique to start with. Multiple solutions (thus sub-optimal ones) are needed. We extend our previous approach to generate multiple sub-optimal solutions that was based on exhaustive enumeration. Here, a sampling approach for multiple RNA interaction is developed. Since not too many samples are needed to reveal solutions that are sufficiently different, sampling provides a much faster alternative. By clustering the sampled solutions, we are able to obtain representatives that correspond to the biologically observed structures. Specifically, our results for the U2-U6 complex and its introns in the spliceosome of yeast, and the CopA-CopT complex in E. Coli are consistent with published biological structures.

Paper Citation

in Harvard Style

Mneimneh S. and Ahmed S. (2016). A Sampling Approach for Multiple RNA Interaction - Finding Sub-optimal Solutions Fast . In Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2016) ISBN 978-989-758-170-0, pages 75-84. DOI: 10.5220/0005707900750084

in Bibtex Style

@conference{bioinformatics16,
author={Saad Mneimneh and Syed Ali Ahmed},
title={A Sampling Approach for Multiple RNA Interaction - Finding Sub-optimal Solutions Fast},
booktitle={Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2016)},
year={2016},
pages={75-84},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005707900750084},
isbn={978-989-758-170-0},
}

in EndNote Style

TY - CONF
JO - Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2016)
TI - A Sampling Approach for Multiple RNA Interaction - Finding Sub-optimal Solutions Fast
SN - 978-989-758-170-0
AU - Mneimneh S.
AU - Ahmed S.
PY - 2016
SP - 75
EP - 84
DO - 10.5220/0005707900750084