RASS: a web server for RNA alignment in the joint sequence-structure space

He, Gewen; Steppi, Albert; Laborde, Jose; Srivastava, Anuj; Zhao, Pei‐Ji; Zhang, Jinfeng

doi:10.1093/nar/gku429

Cited by 8 publications

(13 citation statements)

References 30 publications

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“…In addition, we also ran CARNA [ 14 ], RNA Sampler [ 11 ], DAFS [ 12 ], R3D Align [ 53 ] and RASS [ 37 ] on the 106 pairs of molecules. The CARNA tool was chosen because an option of the tool is closely related to RKalign, both of which can align known pseudoknot structures.…”

Section: Resultsmentioning

confidence: 99%

“…Pseudoknots are part of RNA tertiary motifs [ 2 ]. There are 3D alignment programs that can compare RNA tertiary structures including pseudoknots [ 36 , 37 ]. These programs consider the entire RNA 3D structure as a whole, and accept PDB files with 3D coordinates as input.…”

Section: Discussionmentioning

confidence: 99%

“…Rahrig et al [ 36 ] presented the R3D Align tool for performing global pairwise alignment of RNA 3D structures using local superpositions. He et al [ 37 ] developed the RASS web server for comparing RNA 3D structures using both sequence and 3D structure information. The above methods and tools were mainly designed for aligning two RNA tertiary structures by considering their geometric properties and torsion angles.…”

Section: Introductionmentioning

confidence: 99%

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Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores

et al. 2015

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BackgroundRNA 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.ResultsIn 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.ConclusionsThe 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 materialThe 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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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores

et al. 2015

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“…He et al . [ 36 ] developed the RASS web server for comparing RNA 3D structures using both sequence and 3D structure information.…”

Section: Introductionmentioning

confidence: 99%

CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking

et al. 2016

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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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“…The role of RNA is largely determined by its tertiary structure and the comparison of 3D RNA structures is, thus, an effective tool for studying RNA function and evolutionary relationships. Several methods and servers for pairwise RNA structure comparison and alignment exist, including ARTS [ 8 , 9 ], DIAL [ 10 ], iPARTS [ 11 ], SARA [ 12 , 13 ], SARSA [ 14 ], Rclick [ 15 , 16 ], R3Dalign [ 17 , 18 ], RASS [ 19 ], FRASS [ 20 ], SETTER [ 21 , 22 ] or R3D-BLAST [ 23 ]. The extension of a pairwise alignment to the simultaneous alignment of several structures is called a multiple structure alignment.…”

Section: Introductionmentioning

confidence: 99%

MultiSETTER: web server for multiple RNA structure comparison

2015

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BackgroundUnderstanding 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.ResultsIn 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.ConclusionTo 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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RASS: a web server for RNA alignment in the joint sequence-structure space

Cited by 8 publications

References 30 publications

Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores

Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores

CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking

MultiSETTER: web server for multiple RNA structure comparison

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