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Fast prediction of RNA-RNA interaction

Raheleh Salari, Rolf Backofen, S Cenk Sahinalp
2010 Algorithms for Molecular Biology  
Moreover, we introduce a fast heuristic method to predict the specific (multiple) binding sites of two interacting RNAs.  ...  Methods: In this paper we present a novel algorithm to accurately predict the minimum free energy structure of RNA-RNA interaction under the most general type of interactions studied in the literature.  ...  Conclusions This paper introduce a fast algorithm for RNA-RNA interaction prediction.  ... 
doi:10.1186/1748-7188-5-5 pmid:20047661 pmcid:PMC2828455 fatcat:tu6mdwqknjesfp7dd7kn3pumnm

Fast Prediction of RNA-RNA Interaction [chapter]

Raheleh Salari, Rolf Backofen, S. Cenk Sahinalp
2009 Lecture Notes in Computer Science  
Moreover, we introduce a fast heuristic method to predict the specific (multiple) binding sites of two interacting RNAs.  ...  In this paper we present a novel algorithm to accurately predict the minimum free energy structure of RNA-RNA interaction under the most general type of interactions studied in the literature.  ...  Conclusion In this work, we introduced a fast algorithm for RNA-RNA interaction prediction.  ... 
doi:10.1007/978-3-642-04241-6_22 fatcat:rmtv52t3lbaynmmfrte5a2osby

Fast accessibility-based prediction of RNA–RNA interactions

Hakim Tafer, Fabian Amman, Florian Eggenhofer, Peter F. Stadler, Ivo L. Hofacker
2011 Bioinformatics  
Motivation: Currently, the best RNA-RNA interaction prediction tools are based on approaches that consider both the inter-and intramolecular interactions of hybridizing RNAs.  ...  Results: A new approach for RNA-RNA interaction was developed, with a prediction accuracy that is similar to that of algorithms that explicitly consider intramolecular structures, but running at least  ...  These results emphasize the importance of accessibility for the correct prediction of RNA-RNA interactions.  ... 
doi:10.1093/bioinformatics/btr281 pmid:21593134 fatcat:4zsnxapsjzfhporb57pbzsjv4y

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming

Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu
2010 Computer applications in the biosciences : CABIOS  
Results: We present RactIP, a fast and accurate prediction method for RNA-RNA interaction of general type using integer programming.  ...  Experimental results on real interaction data show that prediction accuracy of RactIP is at least comparable to that of several state-of-the-art methods for RNA-RNA interaction prediction.  ...  Funding: Young Scientists (B) (KAKENHI) from Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan (#22700313 to Y.K., #22700305 to K.S.). Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btq372 pmid:20823308 pmcid:PMC2935440 fatcat:ccnse33vyfcobjpcc5ffxayfoa

An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids [article]

Hamidreza Chitsaz and Elmirasadat Forouzmand and Gholamreza Haffari
2013 arXiv   pre-print
The space complexity of our algorithm is the same as that of sparse folding algorithms, and the time complexity of our algorithm is O(MFE(n)ℓ) for single RNA and O(MFE(m, n)ℓ) for RNA-RNA interaction in  ...  It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model.  ...  In the absence of high throughput experimental assays to observe RNA structure and RNA-RNA interactions, the problems of RNA structure prediction and RNA-RNA interaction prediction gain the highest priority  ... 
arXiv:1301.1590v1 fatcat:qc6rdylds5fv7lkvbw7r5dqymi

An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids

Hamidreza Chitsaz, Elmirasadat Forouzmand, Gholamreza Haffari
2013 Journal of Computational Biology  
The space complexity of our algorithm is the same as that of sparse folding algorithms, and the time complexity of our algorithm is O(M F E(n)ℓ) for single RNA and O(M F E(m, n)ℓ) for RNA-RNA interaction  ...  It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model.  ...  In the absence of high throughput experimental assays to observe RNA structure and RNA-RNA interactions, the problems of RNA structure prediction and RNA-RNA interaction prediction gain the highest priority  ... 
doi:10.1089/cmb.2013.0003 pmid:23829650 fatcat:emvrvcrkirckbkflbrr3dpreay

Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming

Y. Kato, K. Sato, K. Asai, T. Akutsu
2012 Nucleic Acids Research  
We present a web-based tool set Rtips for fast and accurate prediction of RNA 2D complex structures.  ...  Rtips comprises two computational tools based on integer programming, IPknot for predicting RNA secondary structures with pseudoknots and RactIP for predicting RNA-RNA interactions with kissing hairpins  ...  Furthermore, interaction with another RNA or protein is often necessary for functional RNAs to perform their programmed tasks, and prediction of interacting structures is also an important problem in bioinformatics  ... 
doi:10.1093/nar/gks412 pmid:22600734 pmcid:PMC3394313 fatcat:yfg7rgc2zzee5a4b7aj42uj5qe

omiXcore: a web server for prediction of protein interactions with large RNA

Alexandros Armaos, Davide Cirillo, Gian Gaetano Tartaglia, Ivo Hofacker
2017 Bioinformatics  
Our webserver allows (i) use of both protein and RNA sequences without size restriction, (ii) pre-compiled library for exploration of human long intergenic RNAs interactions and (iii) prediction of binding  ...  The method discriminates interacting and non-interacting protein-RNA pairs and identifies RNA binding sites with Areas under the ROC curve > 0.80, which suggests that the tool is particularly useful to  ...  Calibrated on eCLIP data, omiXcore allows fast and quantitative prediction of RBP interactions with human long intergenic RNAs (lincRNAs), facilitating experimental design and analysis.  ... 
doi:10.1093/bioinformatics/btx361 pmid:28637296 pmcid:PMC5870566 fatcat:drqnf7nfmbdchjweepm6zxk6tq

catRAPID omics: a web server for large-scale prediction of protein-RNA interactions

F. Agostini, A. Zanzoni, P. Klus, D. Marchese, D. Cirillo, G. G. Tartaglia
2013 Bioinformatics  
Here we introduce catRAPID omics, a server for largescale calculations of protein-RNA interactions.  ...  Our web server allows (i) predictions at proteomic and transcriptomic level; (ii) use of protein and RNA sequences without size restriction; (iii) analysis of nucleic acid binding regions in proteins;  ...  Our server enables fast calculations of ribonucleoprotein associations and predicts RNA binding activity of proteins with high accuracy, thus resulting in a powerful tool for designing new experiments.  ... 
doi:10.1093/bioinformatics/btt495 pmid:23975767 pmcid:PMC3810848 fatcat:z6kq54re4zg6nmwzlr5q3da7zq

Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA

C. Smith, S. Heyne, A. S. Richter, S. Will, R. Backofen
2010 Nucleic Acids Research  
The tools INTARNA, EXPARNA and LOCARNA support the prediction of RNA-RNA interaction, exact RNA matching and alignment of RNA, respectively.  ...  The Freiburg RNA tools web server integrates three tools for the advanced analysis of RNA in a common web-based user interface.  ...  We also thank all people who have been involved in testing the robustness and functionality of the final web server.  ... 
doi:10.1093/nar/gkq316 pmid:20444875 pmcid:PMC2896085 fatcat:7ztfaqtzlbhy5lue5xjtlpfiry

HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures

2019 Nucleic Acids Research  
It was also found that inclusion of the inter-RNA base-pairing information from RNA-RNA interaction prediction can significantly improve the docking accuracy, especially for the top prediction.  ...  Therefore, determining the complex structures between RNAs/DNAs is crucial to understand the molecular mechanism of related RNA/DNA-RNA/DNA interactions.  ...  Due to the limited number of RNA/DNA structures in the PDB and the difficulty to construct RNA/DNA models, we have also taken advantage of our ab initio method 3dRNA for fast RNA 3D structure prediction  ... 
doi:10.1093/nar/gkz412 pmid:31114906 pmcid:PMC6602492 fatcat:fftyz2w4crapfimyjkqbnhnule

LncTar: a tool for predicting the RNA targets of long noncoding RNAs

Jianwei Li, Wei Ma, Pan Zeng, Junyi Wang, Bin Geng, Jichun Yang, Qinghua Cui
2014 Briefings in Bioinformatics  
Although several methods have been developed to predict RNA-RNA interactions, none of them can be used to predict the RNA targets of lncRNAs in a large scale.  ...  Finally, we believe that LncTar could be an efficient tool for the fast identification of the RNA targets of lncRNAs. LncTar is freely available at http://www.cuilab.cn/lnctar.  ...  In addition, the algorithm of LncTar has a running time ofoðn 2 Þ, which makes it possible for fast and global prediction of the RNA targets for given lncRNAs.  ... 
doi:10.1093/bib/bbu048 pmid:25524864 fatcat:6fjcf56k6vecjajvckeo74po7m

EARLY EVENTS IN RNA FOLDING

D Thirumalai, Namkyung Lee, Sarah A Woodson, DK Klimov
2001 Annual review of physical chemistry (Print)  
A key prediction of our theory is that RNA folding can be described by the kinetic partitioning mechanism (KPM).  ...  Estimates of time scales for the initial events in RNA folding are provided for the Tetrahymena ribozyme.  ...  A consequence of KPM is that the time dependence of a fraction of native RNA should be given by f N (t) = max − e −k fast t − i A i e −k i t , 1. where k fast is the rate for the fast process, k i is the  ... 
doi:10.1146/annurev.physchem.52.1.751 pmid:11326079 fatcat:m6hvaphnbbbg3pjg5tcaan3gwq

Automated and fast building of three-dimensional RNA structures

Yunjie Zhao, Yangyu Huang, Zhou Gong, Yanjie Wang, Jianfen Man, Yi Xiao
2012 Scientific Reports  
It is still a challenge for accurate, automated and fast prediction of tertiary structures of long RNA chains.  ...  Here, we present an automated and fast program,3dRNA, for RNA tertiary structure prediction with reasonable accuracy for RNAs of larger size and complex topology.  ...  It is still a challenge for accurate, automated and fast prediction of tertiary structures of long RNA chains.  ... 
doi:10.1038/srep00734 pmid:23071898 pmcid:PMC3471093 fatcat:wabhkwnptve5big3a3xqhptz7u

PLEXY: efficient target prediction for box C/D snoRNAs

Stephanie Kehr, Sebastian Bartschat, Peter F. Stadler, Hakim Tafer
2010 Computer applications in the biosciences : CABIOS  
Results: PLEXY is a dynamic programming algorithm that computes thermodynamically optimal interactions of a box C/D snoRNA with a putative target RNA.  ...  Motivation: Small nucleolar RNAs (snoRNAs) are an abundant class of non-coding RNAs with a wide variety of cellular functions including chemical modification of RNA, telomere maintanance, pre-rRNA processing  ...  In contrast to RNAcofold used in snoTarget, RNAplex neglects the internal structure of the interacting RNA sequences and hence is fast enough for genomewide searches without the need for additional prefiltering  ... 
doi:10.1093/bioinformatics/btq642 pmid:21076148 fatcat:eilg6jt2gjh67pzmv7jeyt5vly
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