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Chen X, Khan NS, Zhang S. LocalSTAR3D: a local stack-based RNA 3D structural alignment tool. Nucleic Acids Res 2020; 48:e77. [PMID: 32496533 PMCID: PMC7367197 DOI: 10.1093/nar/gkaa453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/15/2020] [Accepted: 05/27/2020] [Indexed: 11/29/2022] Open
Abstract
A fast-growing number of non-coding RNA structures have been resolved and deposited in Protein Data Bank (PDB). In contrast to the wide range of global alignment and motif search tools, there is still a lack of local alignment tools. Among all the global alignment tools for RNA 3D structures, STAR3D has become a valuable tool for its unprecedented speed and accuracy. STAR3D compares the 3D structures of RNA molecules using consecutive base-pairs (stacks) as anchors and generates an optimal global alignment. In this article, we developed a local RNA 3D structural alignment tool, named LocalSTAR3D, which was extended from STAR3D and designed to report multiple local alignments between two RNAs. The benchmarking results show that LocalSTAR3D has better accuracy and coverage than other local alignment tools. Furthermore, the utility of this tool has been demonstrated by rediscovering kink-turn motif instances, conserved domains in group II intron RNAs, and the tRNA mimicry of IRES RNAs.
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Affiliation(s)
- Xiaoli Chen
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Nabila Shahnaz Khan
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
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2
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Zheng J, Xie J, Hong X, Liu S. RMalign: an RNA structural alignment tool based on a novel scoring function RMscore. BMC Genomics 2019; 20:276. [PMID: 30961545 PMCID: PMC6454663 DOI: 10.1186/s12864-019-5631-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 03/20/2019] [Indexed: 01/30/2023] Open
Abstract
Background RNA-protein 3D complex structure prediction is still challenging. Recently, a template-based approach PRIME is proposed in our team to build RNA-protein 3D complex structure models with a higher success rate than computational docking software. However, scoring function of RNA alignment algorithm SARA in PRIME is size-dependent, which limits its ability to detect templates in some cases. Results Herein, we developed a novel RNA 3D structural alignment approach RMalign, which is based on a size-independent scoring function RMscore. The parameter in RMscore is then optimized in randomly selected RNA pairs and phase transition points (from dissimilar to similar) are determined in another randomly selected RNA pairs. In tRNA benchmarking, the precision of RMscore is higher than that of SARAscore (0.88 and 0.78, respectively) with phase transition points. In balance-FSCOR benchmarking, RMalign performed as good as ESA-RNA with a non-normalized score measuring RNA structural similarity. In balance-x-FSCOR benchmarking, RMalign achieves much better than a state-of-the-art RNA 3D structural alignment approach SARA due to a size-independent scoring function. Take the advantage of RMalign, we update our RNA-protein modeling approach PRIME to version 2.0. The PRIME2.0 significantly improves about 10% success rate than PRIME. Conclusion Based on a size-independent scoring function RMscore, a novel RNA 3D structural alignment approach RMalign is developed and integrated into PRIME2.0, which could be useful for the biological community in modeling protein-RNA interaction. Electronic supplementary material The online version of this article (10.1186/s12864-019-5631-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jinfang Zheng
- School of Physics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Juan Xie
- School of Physics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Xu Hong
- School of Physics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Shiyong Liu
- School of Physics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
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3
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Piatkowski P, Jablonska J, Zyla A, Niedzialek D, Matelska D, Jankowska E, Walen T, Dawson WK, Bujnicki JM. SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments. Nucleic Acids Res 2017; 45:e150. [PMID: 28934487 PMCID: PMC5766185 DOI: 10.1093/nar/gkx631] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 07/12/2017] [Indexed: 01/28/2023] Open
Abstract
RNA has been found to play an ever-increasing role in a variety of biological processes. The function of most non-coding RNA molecules depends on their structure. Comparing and classifying macromolecular 3D structures is of crucial importance for structure-based function inference and it is used in the characterization of functional motifs and in structure prediction by comparative modeling. However, compared to the numerous methods for protein structure superposition, there are few tools dedicated to the superimposing of RNA 3D structures. Here, we present SupeRNAlign (v1.3.1), a new method for flexible superposition of RNA 3D structures, and SupeRNAlign-Coffee—a workflow that combines SupeRNAlign with T-Coffee for inferring structure-based sequence alignments. The methods have been benchmarked with eight other methods for RNA structural superposition and alignment. The benchmark included 151 structures from 32 RNA families (with a total of 1734 pairwise superpositions). The accuracy of superpositions was assessed by comparing structure-based sequence alignments to the reference alignments from the Rfam database. SupeRNAlign and SupeRNAlign-Coffee achieved significantly higher scores than most of the benchmarked methods: SupeRNAlign generated the most accurate sequence alignments among the structure superposition methods, and SupeRNAlign-Coffee performed best among the sequence alignment methods.
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Affiliation(s)
- Pawel Piatkowski
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland
| | - Jagoda Jablonska
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland
| | - Adriana Zyla
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland
| | - Dorota Niedzialek
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland
| | - Dorota Matelska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland
| | - Elzbieta Jankowska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland
| | - Tomasz Walen
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland.,Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Wayne K Dawson
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland.,Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznań, Poland
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4
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Yang CH, Shih CT, Chen KT, Lee PH, Tsai PH, Lin JC, Yen CY, Lin TY, Lu CL. iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2. Nucleic Acids Res 2016; 44:W328-32. [PMID: 27185896 PMCID: PMC4987943 DOI: 10.1093/nar/gkw412] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 05/04/2016] [Indexed: 02/02/2023] Open
Abstract
Since its first release in 2010, iPARTS has become a valuable tool for globally or locally aligning two RNA 3D structures. It was implemented by a structural alphabet (SA)-based approach, which uses an SA of 23 letters to reduce RNA 3D structures into 1D sequences of SA letters and applies traditional sequence alignment to these SA-encoded sequences for determining their global or local similarity. In this version, we have re-implemented iPARTS into a new web server iPARTS2 by constructing a totally new SA, which consists of 92 elements with each carrying both information of base and backbone geometry for a representative nucleotide. This SA is significantly different from the one used in iPARTS, because the latter consists of only 23 elements with each carrying only the backbone geometry information of a representative nucleotide. Our experimental results have shown that iPARTS2 outperforms its previous version iPARTS and also achieves better accuracy than other popular tools, such as SARA, SETTER and RASS, in RNA alignment quality and function prediction. iPARTS2 takes as input two RNA 3D structures in the PDB format and outputs their global or local alignments with graphical display. iPARTS2 is now available online at http://genome.cs.nthu.edu.tw/iPARTS2/.
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Affiliation(s)
- Chung-Han Yang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30050, Taiwan Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Cheng-Ting Shih
- Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Kun-Tze Chen
- Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Po-Han Lee
- Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Ping-Han Tsai
- Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Jian-Cheng Lin
- Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Ching-Yu Yen
- Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Tiao-Yin Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Chin Lung Lu
- Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan
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Hua L, Song Y, Kim N, Laing C, Wang JTL, Schlick T. CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking. PLoS One 2016; 11:e0147097. [PMID: 26789998 PMCID: PMC4720362 DOI: 10.1371/journal.pone.0147097] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 12/29/2015] [Indexed: 01/01/2023] Open
Abstract
RNA junctions are important structural elements of RNA molecules. They are formed when three or more helices come together in three-dimensional space. Recent studies have focused on the annotation and prediction of coaxial helical stacking (CHS) motifs within junctions. Here we exploit such predictions to develop an efficient alignment tool to handle RNA secondary structures with CHS motifs. Specifically, we build upon our Junction-Explorer software for predicting coaxial stacking and RNAJAG for modelling junction topologies as tree graphs to incorporate constrained tree matching and dynamic programming algorithms into a new method, called CHSalign, for aligning the secondary structures of RNA molecules containing CHS motifs. Thus, CHSalign is intended to be an efficient alignment tool for RNAs containing similar junctions. Experimental results based on thousands of alignments demonstrate that CHSalign can align two RNA secondary structures containing CHS motifs more accurately than other RNA secondary structure alignment tools. CHSalign yields a high score when aligning two RNA secondary structures with similar CHS motifs or helical arrangement patterns, and a low score otherwise. This new method has been implemented in a web server, and the program is also made freely available, at http://bioinformatics.njit.edu/CHSalign/.
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Affiliation(s)
- Lei Hua
- Bioinformatics Laboratory, Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - Yang Song
- Bioinformatics Laboratory, Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - Namhee Kim
- Department of Chemistry, New York University, New York, New York, United States of America
| | - Christian Laing
- Bioinformatics Laboratory, Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - Jason T. L. Wang
- Bioinformatics Laboratory, Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, United States of America
- * E-mail: (JW); (TS)
| | - Tamar Schlick
- Department of Chemistry, New York University, New York, New York, United States of America
- Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America
- * E-mail: (JW); (TS)
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Čech P, Hoksza D, Svozil D. MultiSETTER: web server for multiple RNA structure comparison. BMC Bioinformatics 2015; 16:253. [PMID: 26264783 PMCID: PMC4531852 DOI: 10.1186/s12859-015-0696-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/05/2015] [Indexed: 12/03/2022] Open
Abstract
Background Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. Results In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. Conclusion To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.
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Affiliation(s)
- Petr Čech
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28, Prague, Czech Republic
| | - David Hoksza
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28, Prague, Czech Republic. .,Department of Software Engineering, Faculty of Mathematics and Physics, Charles University in Prague, Malostranské nám. 25, CZ-118 00, Prague, Czech Republic.
| | - Daniel Svozil
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28, Prague, Czech Republic.
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7
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Song Y, Hua L, Shapiro BA, Wang JTL. Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores. BMC Bioinformatics 2015; 16:39. [PMID: 25727492 PMCID: PMC4339682 DOI: 10.1186/s12859-015-0464-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 01/13/2015] [Indexed: 11/18/2022] Open
Abstract
Background RNA pseudoknots play important roles in many biological processes. Previous methods for comparative pseudoknot analysis mainly focus on simultaneous folding and alignment of RNA sequences. Little work has been done to align two known RNA secondary structures with pseudoknots taking into account both sequence and structure information of the two RNAs. Results In this article we present a novel method for aligning two known RNA secondary structures with pseudoknots. We adopt the partition function methodology to calculate the posterior log-odds scores of the alignments between bases or base pairs of the two RNAs with a dynamic programming algorithm. The posterior log-odds scores are then used to calculate the expected accuracy of an alignment between the RNAs. The goal is to find an optimal alignment with the maximum expected accuracy. We present a heuristic to achieve this goal. The performance of our method is investigated and compared with existing tools for RNA structure alignment. An extension of the method to multiple alignment of pseudoknot structures is also discussed. Conclusions The method described here has been implemented in a tool named RKalign, which is freely accessible on the Internet. As more and more pseudoknots are revealed, collected and stored in public databases, we anticipate a tool like RKalign will play a significant role in data comparison, annotation, analysis, and retrieval in these databases. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0464-9) contains supplementary material, which is available to authorized users.
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