BkTree:
Prediction of RNA 3D Structures with Backbone k-Tree Model


Overview

BkTree is an utility capable of predicting all familites of RNA nucleotide interactions, including base-base, base-phosphate, base-ribose, and base-stacking interactions, from the input query sequence (along with predicted or known canonical Watson-Crick base pairs). The information of predicted nucleotide interactions can be directly used to model a 3D conformation as the predicted 3D stucture for the query RNA sequence.


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BkTree supports RNA sequences with less than 250 nucleotides; the machine that runs this verion of the program needs at least 20 gigabytes of memory. BkTree was coded with Java and C++. It was compiled with Java compiler version 7, C++ compiler version: g++ 4.6.4, and Boost_1_54_0 Libiary.

This package is for Linux platform. It has been compiled and tested on Ubuntu 12.04 and Redhat Fedora Release 20 platforms.


Citation

  • [Ding et al., 2015] Ding, L., Xue, X., LaMarca, S., Mohebbi, M., Samad, A., Malmberg, R.L., Cai, L. (2015) Accurate Prediction of RNA Nucleotide Interactions with Backbone k-Tree Model. Bioinformatics 2015, doi: 10.1093/bioinformatics/btv210.

Related Publication

  • [Ding et al., 2016b] Ding, L., LaMarca, S., Yan, H., Wicker, M., Malmberg, R.L., Momany, C., and Cai, L. (2016) RNA SNAPTree: A Webserver for RNA Nucleotide Interactions and 3D Structure Prediction. in revision.
  • [Ding et al., 2014] Ding, L., Samad, A., Xue, X., Huang, X., Malmberg, R.L., Cai, L. (2014) Stochastic k-tree grammar and its applications in biomolecular structure modeling, Lecture Notes in Computer Science Vol 8370, 308-322.
  • [Ding et al., 2014a] Ding, L., Xue, X., LaMarca, S., Mohebbi, M., Samad, A., Malmberg, R.L., Cai, L. (2014) Ab initio Prediction of RNA Nucleotide Interactions with Backbone k-Tree Model. Proceedings of ECCB'14 Workshop on Computational Methods for Structural RNAs, Strasbourg France, 25-42.