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Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

Stefan E Seemann, Andreas S Richter, Jan Gorodkin, Rolf Backofen
2010 Algorithms for Molecular Biology  
Predicting these RNA interactions is essential for functional studies of putative ncRNAs or for the design of artificial RNAs.  ...  One of the advantages of our approach (in contrast to other RNA-RNA interaction prediction methods) is the application of covariance detection and prediction of pseudoknots between intra-and inter-molecular  ...  Acknowledgements We thank Bjarne Knudsen for inspiring discussions about extensions of the Pfold method.  ... 
doi:10.1186/1748-7188-5-22 pmid:20492641 pmcid:PMC2903599 fatcat:jcqjghofgbctjcktpy3nbar5bm

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences

S. E. Seemann, P. Menzel, R. Backofen, J. Gorodkin
2011 Nucleic Acids Research  
We present web servers to analyze multiple RNA sequences for common RNA structure and for RNA interaction sites.  ...  Thus, an accurate prediction of secondary structure and RNA-RNA interaction is essential for the understanding of biological roles and pathways associated with a specific RNA gene.  ...  ACKNOWLEDGEMENTS We thank Bjarne Knudsen and the Vienna RNA community for Pfold, RNAfold and applied graphical tools. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkr248 pmid:21609960 pmcid:PMC3125731 fatcat:rlo6umo7cbbhfocfrh5fhyrn3i

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

Stefan E. Seemann, Andreas S. Richter, Tanja Gesell, Rolf Backofen, Jan Gorodkin
2010 Computer applications in the biosciences : CABIOS  
Existing methods for the prediction of interactions are all based on single sequences.  ...  We implement a method, PETcofold, that can take covariance information in intra-molecular and intermolecular base pairs into account to predict interactions and secondary structures of two multiple alignments  ...  ACKNOWLEDGEMENTS We thank Jakob Hull Havgaard for his assistance with the evaluation of the predictions. We further thank Sita Lange and Larry Croft for their comments on the manuscript.  ... 
doi:10.1093/bioinformatics/btq634 pmid:21088024 pmcid:PMC3018821 fatcat:2mw4rvki55fkdpyvodt3tlpt2y

Computational approaches to 3D modeling of RNA

Christian Laing, Tamar Schlick
2010 Journal of Physics: Condensed Matter  
To evaluate the performance of the most recent RNA 3D folding algorithms, we provide a comparative study in order to test the performance of available 3D structure prediction algorithms for an RNA data  ...  Since the structural features of RNA are of major importance to their biological function, there is much interest in predicting RNA structure, either in free form or in interaction with various ligands  ...  The authors thank Abdul Iqbal, Yoon Ha, and Segun Jung for their help with data preparation, and Bruce Shapiro for a critical reading of this manuscript.  ... 
doi:10.1088/0953-8984/22/28/283101 pmid:21399271 pmcid:PMC6286080 fatcat:kjgzb26n2vardnhw6jnrbdus7y

Challenges and Approaches to Predicting RNA with Multiple Functional Structures

Susan J Schroeder
2018 RNA: A publication of the RNA Society  
These examples highlight the different approaches and challenges in predicting structure and function from sequence for RNA with multiple biological roles and folds.  ...  More well-defined examples and new metrics for measuring differences in RNA structures will guide future improvements in prediction of RNA structure and function from sequence.  ...  ACKNOWLEDGMENTS This work has been supported by the Burroughs Wellcome Fund (81309).  ... 
doi:10.1261/rna.067827.118 pmid:30143552 pmcid:PMC6239171 fatcat:xdelpczxufb7vksxa7vtierot4

Computational RNA Structure Prediction

Marc Marti-Renom, Emidio Capriotti
2008 Current Bioinformatics  
In this review, we outline the general principles that govern RNA structure and describe the databases and algorithms for analyzing and predicting RNA secondary and tertiary structure.  ...  Despite advances in understanding the folding and unfolding of RNA, our knowledge of the atomic mechanism by which RNA molecules adopt their biological active structure is still limited.  ...  RNA SECONDARY STRUCTURE PREDICTION Single Sequence Free Energy Calculations The RNA folding process is hierarchical [83] , which means that local interactions occur first and are energetically stronger  ... 
doi:10.2174/157489308783329823 fatcat:rpo3hjt2nzgkzdgkhumwz7kmou

Advances in RNA Structure Prediction from Sequence: New Tools for Generating Hypotheses about Viral RNA Structure-Function Relationships

S. J. Schroeder
2009 Journal of Virology  
The RNA sequence contains many layers of information. RNA sequences code for proteins and small RNAs, such as microRNAs or transacting small interfering RNAs (siRNAs).  ...  The tertiary structure contains the interaction sites for proteins, other RNA molecules, carbohydrates, or other small molecules and thus determines the quaternary or higher-order structure.  ...  ACKNOWLEDGMENTS The author is supported by grants from the Oklahoma Center for the Advancement of Science and Technology and the Pharmaceutical Research and Manufacturers of America Foundation and by an  ... 
doi:10.1128/jvi.00251-09 pmid:19369331 pmcid:PMC2698544 fatcat:lipacoqb45hkrdvrxyr6x7ibjy

Towards Long-Range RNA Structure Prediction in Eukaryotic Genes

Dmitri Pervouchine
2018 Genes  
Most comparative methods implement the "first-align-then-fold" principle, i.e., they operate on multiple sequence alignments, while functional RNA structures often reside in non-conserved parts of the  ...  While the local RNA structure can be predicted reasonably well for short sequences, long-range structure at the scale of eukaryotic genes remains problematic from the computational standpoint.  ...  I also acknowledge the organizers and participants of Benasque RNA workshop for inspiring and very motivating meetings. Conflicts of Interest: The author declares no conflict of interest.  ... 
doi:10.3390/genes9060302 pmid:29914113 pmcid:PMC6027157 fatcat:ded2rd7bfndithakhpfowu4twy

Opportunities and Challenges in RNA Structural Modeling and Design

Tamar Schlick, Anna Marie Pyle
2017 Biophysical Journal  
Topics include fundamental processes of RNA, such as structural assemblies (hierarchical folding, multiple conformational states and their clustering), RNA motifs, and chemical reactivity of RNA, as used  ...  We also highlight the software and database issues associated with RNA structures, such as the multiple approaches for motif annotation, the need for frequent database updating, and the importance of quality  ...  We are grateful for partial support of the workshop by the National Institute of General Medical Sciences (NIGMS) award No.  ... 
doi:10.1016/j.bpj.2016.12.037 pmid:28162235 pmcid:PMC5529161 fatcat:i55b65jtybhfrhxnskde3umbvm

RNA structure prediction: Progress and perspective

Ya-Zhou Shi, Yuan-Yan Wu, Feng-Hua Wang, Zhi-Jie Tan
2014 Chinese Physics B  
In this review, the progress in computational models for RNA structure prediction is introduced and the distinguishing features of many outstanding algorithms are discussed, emphasizing three dimensional  ...  A promising coarse-grained model for predicting RNA 3D structure, stability and salt effect is also introduced briefly. Finally, we discuss the major challenges in the RNA 3D structure modeling.  ...  Acknowledgments We are grateful to Shi-Jie Chen, Wenbing Zhang, and Song Cao for valuable discussions.  ... 
doi:10.1088/1674-1056/23/7/078701 fatcat:6pgevfzohrcrrbzqydp3g67sju

Mining small RNA structure elements in untranslated regions of human and mouse mRNAs using structure-based alignment

Mugdha Khaladkar, Jianghui Liu, Dongrong Wen, Jason TL Wang, Bin Tian
2008 BMC Genomics  
This approach resulted in 90 distinct RNA structure groups containing 748 structures, with HSL3 and IRE among the top hits based on conservation of structure.  ...  UnTranslated Regions (UTRs) of mRNAs contain regulatory elements for various aspects of mRNA metabolism, such as mRNA localization, translation, and mRNA stability.  ...  This work was partially supported by a grant from The Foundation of University of Medicine and Dentistry of New Jersey to BT.  ... 
doi:10.1186/1471-2164-9-189 pmid:18439287 pmcid:PMC2413145 fatcat:vh3txhw4ibh2jnuuegnxzo4clq

Analysis and classification of RNA tertiary structures

M. Abraham, O. Dror, R. Nussinov, H. J. Wolfson
2008 RNA: A publication of the RNA Society  
The analysis reveals the current structural repertoire of RNA and exposes common global folds and local tertiary motifs.  ...  This should be beneficial for structure prediction and for gaining insights into structure-function relationships. ; fax: 972-3-640 6476. Article published online ahead of print.  ...  (B) A multiple sequence alignment generated by Clustal W for the four representative structures of the 5S ribosomal RNA cluster.  ... 
doi:10.1261/rna.853208 pmid:18824509 pmcid:PMC2578864 fatcat:pntnjjyldjhztchlrverxwy7tm

Computational analysis of noncoding RNAs

Stefan Washietl, Sebastian Will, David A. Hendrix, Loyal A. Goff, John L. Rinn, Bonnie Berger, Manolis Kellis
2012 Wiley Interdisciplinary Reviews - RNA  
The topics covered include basic and advanced techniques to predict RNA structures, annotation of noncoding RNAs in genomic data, mining RNA-seq data for novel transcripts and prediction of transcript  ...  Noncoding RNAs have emerged as important key players in the cell. Understanding their surprisingly diverse range of functions is challenging for experimental and computational biology.  ...  Finally, several approaches predict conserved interactions between multiple sequence alignments. 78, 79 Kinetic Folding Common structure prediction methods assume that the functional RNA structure  ... 
doi:10.1002/wrna.1134 pmid:22991327 pmcid:PMC3472101 fatcat:vj4kuf777jdxtbbztbrhk5rvl4

Predicting and Modeling RNA Architecture

E. Westhof, B. Masquida, F. Jossinet
2010 Cold Spring Harbor Perspectives in Biology  
The method exploits the modularity and the hierarchical folding of RNA architecture that is viewed as the assembly of preformed double-stranded helices defined by Watson-Crick base pairs and RNA modules  ...  The Assemble integrated suite of computer tools allows for sequence and structure analysis as well as interactive modeling by homology or ab initio assembly with possibilities for fitting within electronic  ...  INTRODUCTION In this article, a general approach for predicting threedimensional (3D) contacts and modeling the architecture of large and structured RNA molecules on the basis of sequence analysis and  ... 
doi:10.1101/cshperspect.a003632 pmid:20504963 pmcid:PMC3039537 fatcat:qxrfw43vkzh4fdprufwsdwfzxu

RNA-RNA interaction prediction based on multiple sequence alignments [article]

Andrew X. Li, Manja Marz, Jing Qin, Christian M.Reidys
2010 arXiv   pre-print
Many computerized methods for RNA-RNA interaction structure prediction have been developed.  ...  We present the a priori folding algorithm ripalign, whose input consists of two (given) multiple sequence alignments (MSA). ripalign outputs (1) the partition function, (2) base-pairing probabilities,  ...  Huang and Jan Engelhardt for helpful suggestions. We thank Sharon Selzo of the Modular and BICoC Benchmark Center, IBM and Kathy Tzeng of IBM Life Sciences Solutions Enablement.  ... 
arXiv:1003.3987v3 fatcat:gqw6yxot55eo3mycsumu4vuune
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