Comparison of Similar RNA 3D Structures and Substructures Search Tools
DOI:
https://doi.org/10.11113/mjfas.v16n4.1741Keywords:
RNA 3D structures, RAG-3D, R3D-BLAST2, FASTR3D, RNA FRABASE 2.0, ARTSAbstract
ncRNAs functions in the cells has produced exponentially increasing data of RNA 3D structures in both PDB and NDB. Tools are needed to search for similar RNA 3D structures in hope to aid with annotation processes. In this article, five tools (ARTS, FASTR3D, RNA FRABASE 2.0, RAG-3D, and R3D-BLAST2) will be compared based on their performances in analyzing samples of RNA 3D structures in different sizes (pseudoknot, 5S rRNA, and 18S rRNA). ARTS was found to be the most outdated and slow tools, while FASTR3D and RNA FRABASE 2.0 is commonly used as a benchmarking standard. RAG-3D & R3D-BLAST2 produces results with the highest accuracy and is still relevant in the present, however, RAG-3D is found to be limited to analyze RNA 3D structures to a certain size (it cannot process very large samples). This article also provides suggestion for future studies to create tools with similar purposes.
References
Eddy, S. R. (2001). Non-coding RNA genes and the modern RNA world. Nature Reviews Genetics, 2(12), 919–929.
Mattick, J. S., Makunin, I. V. (2006). Non-coding RNA. Human Molecular Genetics, 15(1), R17–R29.
Rose, P. W., Prlić, A., Bi, C., Bluhm, W. F., Christie, C. H., Dutta, S., Green, R. K., Goodsell, D. S., Westbrook, J. D., Woo, J., Young, J., Zardecki, C., Berman, H. M., Bourne, P. E., Burley, S. K. (2015). The RCSB Protein Data Bank: views of structureal biology for basic and applied research and education. Nucleid Acids Research, 43, D345–D356.
Narayanan, B. C., Westbrook, J., Ghosh, S., Petrov, A. I., Sweeney, B., Zirbel, C. L., Leontis, N. B., Berman, H. M. (2014). The Nucleic Acid Database: new features and capabilities. Nucleic Acids Research, 42, D114–D122.
Zahran, M., Bayrak, C. S., Elmetwaly, S., Schlick, T. (2015). RAG-3D: a search tool for RNA 3D substructures. Nucleic Acids Research, 43(19), 9474–9488.
Yen, C. Y., Lin, J. C., Chen, K. T., Lu, C. L. (2017). R3D-BLAST2: An improved search tool for similar RNA 3D substructures. BMC Bioinformatics, 18(S16), 574.
Dror, O., Nussinov, R., Wolfson, H. (2005). ARTS: alignment of RNA tertiary structures. Bioinformatics, 21(S2), ii47–ii53.
Abraham, M., Dror, O., Nussinov, R., Wolfson, H. J. (2008). Analysis and classification of RNA tertiary structures. RNA, 14(11), 2274–2289.
Lai, C. E., Tsai, M. Y., Liu, Y. C., Wang, C. W., Chen, K. T., Lu, C. L. (2009). FASTR3D: a fast and accurate search tool for similar RNA 3D structures. Nucleic Acids Research, 37, W287–W295.
Popenda, M., Szachniuk, M., Blazewicz, M., Wasik, S., Burke, E. K., Blazewicz, J., Adamiak, R. W. (2010). RNA FRABASE 2.0: An advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. BMC Bioinformatics, 11(1), 231.
Popenda, M., Blazewicz, M., Szachniuk, M., Adamiak, R. W. (2007). RNA FRABASE version 1.0: An engine with a database to search for the three-dimensional fragments within RNA structures. Nucleic Acids Research, 36, D386–D391.
