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The language of RNA: a formal grammar that includes pseudoknots

E. Rivas, S. R. Eddy
2000 Bioinformatics  
The pseudoknot grammar avoids the use of general context-sensitive rules by introducing a small number of auxiliary symbols used to reorder the strings generated by an otherwise context-free grammar.  ...  This formal representation of the residue correlations in RNA structure is important because it means we can build full probabilistic models of RNA secondary structure, including pseudoknots, and use them  ...  E.R. acknowledges the support of a postdoctoral fellowship granted by the Sloan foundation. We thank an anonymous reviewer for detailed and useful comments.  ... 
doi:10.1093/bioinformatics/16.4.334 pmid:10869031 fatcat:zltiiers3je2ti5onwoidld6cy

Stochastic modeling of RNA pseudoknotted structures: a grammatical approach

L. Cai, R. L. Malmberg, Y. Wu
2003 Bioinformatics  
Methods have previously been developed to model RNA stem-loops successfully using stochastic context-free grammars (SCFG) adapted from computational linguistics; however, the additional complexity of pseudoknots  ...  Our new approach can specify pseudoknotted structures, while avoiding context-sensitive rules, using a single CFG synchronized with a number of regular grammars.  ...  ACKNOWLEDGEMENT We thank the anonymous referees for helpful comments on the earlier version of this paper.  ... 
doi:10.1093/bioinformatics/btg1007 pmid:12855439 fatcat:w3rwyt7igrbwpdyxhtzgabk37m

Memory efficient alignment between RNA sequences and stochastic grammar models of pseudoknots

Yinglei Song, Chunmei Liu, Russell L. Malmberg, Congzhou He, Liming Cai
2006 International Journal of Bioinformatics Research and Applications  
Stochastic Context-Free Grammars (SCFG) has been shown to be effective in modelling RNA secondary structure for searches.  ...  ., 2003) in Stochastic Parallel Communicating Grammar Systems (SPCGS) has extended SCFG to model RNA pseudoknots. However, the alignment algorithm requires O(n 4 ) memory for a sequence of length n.  ...  Table 1 shows a PCGS model of RNA pseudoknots. The model includes a master context-free component G 0 and three auxiliary regular grammar components G 1 , G 2 , and G 3 .  ... 
doi:10.1504/ijbra.2006.010606 pmid:18048167 fatcat:ggxwyhsghrbrvotlzhbmpo4tty

RNA Pseudoknot Folding through Inference and Identification Using TAGRNA [chapter]

Sahar Al Seesi, Sanguthevar Rajasekaran, Reda Ammar
2009 Lecture Notes in Computer Science  
The inferred grammars are used to indentify sequences with structures analogous to those in the training set and generate a folding for these sequences.  ...  After being ignored for a long time due to the high computational complexity it requires, pseudoknot is one type of RNA structures that has been given a lot of attention lately.  ...  Also, pseudoknots cannot be modeled with Context Free Grammars (CFG) due to the crossing dependencies of their bps.  ... 
doi:10.1007/978-3-642-00727-9_11 fatcat:u5nvx7mq3fdslo6yv32fo27p54

Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures

H. Matsui, K. Sato, Y. Sakakibara
2005 Bioinformatics  
On the other hand, tree adjoining grammars (TAGs) is a subclass of context-sensitive grammar, which is suitable for modeling pseudoknots.  ...  Results: We propose the pair stochastic tree adjoining grammars (PSTAGs) for modeling RNA secondary structures including pseudoknots and show the strong experimental evidences that modeling pseudoknot  ...  What makes pseudoknots so difficult to be handled is the fact that modeling the pseudoknot structures of RNAs is beyond the generative power of context-free grammars, and inevitably involves in the hard  ... 
doi:10.1093/bioinformatics/bti385 pmid:15784748 fatcat:4ll2s4zrt5aftf4bdghfbivcsy

Pseudoknot Identification through Learning TAGRNA [chapter]

Sahar Al Seesi, Sanguthevar Rajasekaran, Reda Ammar
2008 Lecture Notes in Computer Science  
Pseudoknot is one type of RNA structures that cannot be modeled with Context Free Grammars (CFG) because it exhibits crossing dependencies.  ...  We present the results of using the proposed framework for identifying RNA sequences with pseudoknot structures.  ...  Pseudoknot is one type of RNA structures that cannot be modeled with Context Free Grammars (CFG) because it exhibits crossing dependencies.  ... 
doi:10.1007/978-3-540-88436-1_12 fatcat:bfshc24rjna4jaa7e4vnyzstdi

Alignment of noncoding ribonucleic acids with pseudoknots using context-sensitive hidden Markov model

Mousa Shamsi, NayyerMostaghim Bakhshayesh, MohammadHossein Sedaaghi, Hossein Ebrahimnezhad
2019 Journal of Medical Signals & Sensors  
The main purpose of this study was to design a suitable algorithm based on context-sensitive hidden Markov models (csHMMs) for the alignment of secondary structures of RNAs, which can identify noncoding  ...  The alignment results for RNAs belonging to the hepatitis delta virus family showed an accuracy of 83.33%, a specificity of 89%, and a sensitivity of 97%, and RNAs belonging to the purine family showed  ...  The proposed model in this article, based on the context-sensitive HMM (csHMM) that uses this algorithm, can be provided a framework for the alignment of RNA secondary structures including pseudoknots  ... 
doi:10.4103/jmss.jmss_11_19 pmid:31737554 pmcid:PMC6839439 fatcat:ga2jtbdtmbdvjjxasgy2q7eq6q

Evolving state grammar for modeling DNA and RNA structures

Ajay Kumar, Nidhi Kalra, Sunita Garhwal
2017 International Journal of Engineering & Technology  
Another major advantage of the proposed approach is state grammar can be represented by deep pushdown automata, whereas no such automaton exists for matrix ins-del system.  ...  In this paper, we represent bio-molecular structures (Attenuator, Extended Pseudoknot Structure, Kissing Hairpin, Simple H-type structure, Recursive Pseudoknot and Three-knot Structure) using state grammar  ...  Kuppusamy as their research work help us in understanding state grammar and Bio-molecular structures.  ... 
doi:10.14419/ijet.v7i1.8627 fatcat:enlsf5es3ncsfkoertdc4bbrki

Recent Progresses in the Linguistic Modeling of Biological Sequences Based on Formal Language Theory

Hyun-Seok Park, Bulgan Galbadrakh, Young-Mi Kim
2011 Genomics & Informatics  
Grammars used in this way would constitute a model of underlying biological processes or structures, and that grammars may, in fact, serve as an appropriate tool for theory formation.  ...  The intent of this review is therefore to list some bibliographic references regarding the recent progresses in the field of grammatical modeling of biological sequences.  ...  This work was partly sponsored by the Korean government scholarship program of NIIED (National Institute of International Education) and the industry-university cooperation program of SMBA (Small and Medium  ... 
doi:10.5808/gi.2011.9.1.005 fatcat:5xcv4fhfh5bu3cedb7dhexabfm

Prediction of RNA Pseudoknotted Secondary Structure using Stochastic Context Free Grammars (SCFG)1

Rafael García
2006 CLEI Electronic Journal  
Previously, a model adapted from computational linguistics – Stochastic Context Free Grammars (SCFG) – has been used to predict RNA secondary structure.  ...  However, to this date the SCFG approach impose a prohibitive complexity cost [O(n4)] when they are applied to the prediction of pseudoknots, mainly because a context-sensitive grammar is formally required  ...  Acknowledgments We gratefully acknowledge Carlos Jaramillo, for his multiple and patient conversations over molecular biology, and Rafael Gómez, for his inspiring suggestions about an integrated view of  ... 
doi:10.19153/cleiej.9.2.6 fatcat:y55icxerojg6lce7nrnzi5b3wa

Efficient known ncRNA search including pseudoknots

Cheng Yuan, Yanni Sun
2013 BMC Bioinformatics  
However, the state-of-the-art known ncRNA search is based on context-free grammar (CFG), which cannot effectively model pseudoknots.  ...  Searching for members of characterized ncRNA families containing pseudoknots is an important component of genome-scale ncRNA annotation.  ...  Acknowledgements This work was partially supported by the NSF grants DBI-0953738 and IOS-1126998. Declarations The publication costs for this article were funded by NSF DBI-0953738 and IOS-1126998.  ... 
doi:10.1186/1471-2105-14-s2-s25 pmid:23369049 pmcid:PMC3549841 fatcat:chkq7mexwzg3fbdbpxbapl34xm

Computational identification and analysis of noncoding RNAs - Unearthing the buried treasures in the genorne

Byung-Jun Yoon, P.P. Vaidyanathan
2007 IEEE Signal Processing Magazine  
Grammars Regular Grammars Context-Free Grammars 1(b), RNA pseudoknots have crossing dependencies between bases, and to model such dependencies we have to resort to more complex models such as the context-sensitive  ...  [28] uses tree adjoining grammars (TAGs) for modeling pseudoknots.  ... 
doi:10.1109/msp.2007.273058 fatcat:er6ktap6bnaxvmhe4l56etc7l4

Predicting RNA secondary structures with pseudoknots by MCMC sampling

Dirk Metzler, Markus E. Nebel
2007 Journal of Mathematical Biology  
Allowing all possible configurations of pseudoknots is not compatible with context-free grammar models and makes the search for an optimal secondary structure NP-complete.  ...  The most probable secondary structure of an RNA molecule, given the nucleotide sequence, can be computed efficiently if a stochastic context-free grammar (SCFG) is used as the prior distribution of the  ...  Acknowledgments We would like to thank two anonymous referees for very helpful suggestions and Martina Fröhlich for preprocessing the tmRNA data.  ... 
doi:10.1007/s00285-007-0106-6 pmid:17589847 fatcat:oi3a2zsdwbgn5iy4opfditnsue

Structural Alignment of RNAs Using Profile-csHMMs and Its Application to RNA Homology Search: Overview and New Results

Byung-Jun Yoon, P. P. Vaidyanathan
2008 IEEE Transactions on Automatic Control  
In this paper, we propose a new method for representing RNA sequence profiles and finding structural alignment of RNAs based on profile context-sensitive hidden Markov models (profile-csHMMs).  ...  Unlike existing models, the proposed approach can handle any kind of RNA secondary structures, including pseudoknots.  ...  Instead of using these grammars, we can use the context-sensitive HMMs that have been recently proposed [32] , [37] .  ... 
doi:10.1109/tac.2007.911322 fatcat:i4fegeytpjc2bfjumz7zhuuuw4

Structural Alignment of RNAs Using Profile-csHMMs and Its Application to RNA homology Search: Overview and New Results

B.-J. Yoon, P. P. Vaidyanathan
2009 IEEE Transactions on Circuits and Systems I Fundamental Theory and Applications  
In this paper, we propose a new method for representing RNA sequence profiles and finding structural alignment of RNAs based on profile context-sensitive hidden Markov models (profile-csHMMs).  ...  Unlike existing models, the proposed approach can handle any kind of RNA secondary structures, including pseudoknots.  ...  Instead of using these grammars, we can use the context-sensitive HMMs that have been recently proposed [32] , [37] .  ... 
doi:10.1109/tcsi.2007.911322 fatcat:cy4thm2aofhizd7cnv6jp7ozmm
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