Sha Gong1,2, Chengxin Zhang2, Yang Zhang2,3. 1. School of Physics and Electronic Information, Huanggang Normal University, Huanggang, China. 2. Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA. 3. Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
Abstract
MOTIVATION: Comparison of RNA 3D structures can be used to infer functional relationship of RNA molecules. Most of the current RNA structure alignment programs are built on size-dependent scales, which complicate the interpretation of structure and functional relations. Meanwhile, the low speed prevents the programs from being applied to large-scale RNA structural database search. RESULTS: We developed an open-source algorithm, RNA-align, for RNA 3D structure alignment which has the structure similarity scaled by a size-independent and statistically interpretable scoring metric. Large-scale benchmark tests show that RNA-align significantly outperforms other state-of-the-art programs in both alignment accuracy and running speed. The major advantage of RNA-align lies at the quick convergence of the heuristic alignment iterations and the coarse-grained secondary structure assignment, both of which are crucial to the speed and accuracy of RNA structure alignments. AVAILABILITY AND IMPLEMENTATION: https://zhanglab.ccmb.med.umich.edu/RNA-align/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Comparison of RNA 3D structures can be used to infer functional relationship of RNA molecules. Most of the current RNA structure alignment programs are built on size-dependent scales, which complicate the interpretation of structure and functional relations. Meanwhile, the low speed prevents the programs from being applied to large-scale RNA structural database search. RESULTS: We developed an open-source algorithm, RNA-align, for RNA 3D structure alignment which has the structure similarity scaled by a size-independent and statistically interpretable scoring metric. Large-scale benchmark tests show that RNA-align significantly outperforms other state-of-the-art programs in both alignment accuracy and running speed. The major advantage of RNA-align lies at the quick convergence of the heuristic alignment iterations and the coarse-grained secondary structure assignment, both of which are crucial to the speed and accuracy of RNA structure alignments. AVAILABILITY AND IMPLEMENTATION: https://zhanglab.ccmb.med.umich.edu/RNA-align/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Ioanna Kalvari; Joanna Argasinska; Natalia Quinones-Olvera; Eric P Nawrocki; Elena Rivas; Sean R Eddy; Alex Bateman; Robert D Finn; Anton I Petrov Journal: Nucleic Acids Res Date: 2018-01-04 Impact factor: 16.971
Authors: Michael H D'Souza; Tyler Mrozowich; Maulik D Badmalia; Mitchell Geeraert; Angela Frederickson; Amy Henrickson; Borries Demeler; Michael T Wolfinger; Trushar R Patel Journal: Nucleic Acids Res Date: 2022-06-10 Impact factor: 19.160