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An optimized parsing algorithm well suited to RNA folding

F Lefebvre
1995 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
The application of stochastic context-free grammars to the determination of RNA foldings allows a simple description of the sub-class of sought secondary structures, but it needs efficient parsing algorithms  ...  The more classic thermodynamic model of folding, popularized by Zuker under the framework of dynamic programming algorithms, allows an easy computation of foldings but its use is delicate when constraints  ...  In some sense, our tabular GCP parsing algorithm is an optimal tabular parsing algorithm. Theorem 2 The time complexity of algorithm I is O(n a) and its space complexity is O(n2).  ... 
pmid:7584441 fatcat:uasx7rllpjeppeaexlqssa44dy

A max-margin model for efficient simultaneous alignment and folding of RNA sequences

C. B. Do, C.-S. Foo, S. Batzoglou
2008 Bioinformatics  
In this work, we present RAF (RNA Alignment and Folding), an efficient algorithm for simultaneous alignment and consensus folding of unaligned RNA sequences.  ...  Algorithmically, RAF exploits sparsity in the set of likely pairing and alignment candidates for each nucleotide (as identified by the CONTRAfold or CONTRAlign programs) to achieve an effectively quadratic  ...  ACKNOWLEDGEMENTS C.B.D. was supported by an NSF Graduate Research Fellowship. C.S.F. was supported by an A*STAR National Science Scholarship.  ... 
doi:10.1093/bioinformatics/btn177 pmid:18586747 pmcid:PMC2718655 fatcat:ac3x3kr76fep7czpkurpzafy4y

A grammar-based unification of several alignment and folding algorithms

F Lefebvre
1996 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
To complete this formalism, we designed and implemented a tool which, given a MTSAG, will output an efficient parser for this grammar.  ...  We show in this paper that many popular models of folding and/or alignment may be described by a new formalism: multi-tape S-attribute grammars (MT-SAG's).  ...  Acknowledgments I wish to thank D. Gardy and J.-M. Steyaert for useful suggestions and comments. I am grateful to L. Grate for data on UCSC's SCFG experiments and F.  ... 
pmid:8877514 fatcat:yiq457ouhnhuvggcmcwx7wkai4

Explaining and Controlling Ambiguity in Dynamic Programming [chapter]

Robert Giegerich
2000 Lecture Notes in Computer Science  
We demonstrate the advantages of such a systematic approach using problems from the areas of RNA folding and pairwise sequence comparison.  ...  W e argue that the use of canonical yield grammars leads to transparent and versatile dynamic programming algorithms.  ...  Two Classical DP Algorithms in ADP Notation Zuker's Algorithm for RNA folding.  ... 
doi:10.1007/3-540-45123-4_6 fatcat:mhgiegbm2zg7podqxpwjmlk4fi

RNA movies: visualizing RNA secondary structure spaces

D Evers, R Giegerich
1999 Bioinformatics  
Results: RNA Movies has been used to generate animations of a switching structure in the spliced leader RNA of Leptomonas collosoma and sequential foldings of potato spindle tuber viroid transcripts.  ...  In this way, it creates the impression of an RNA molecule exploring its own two-dimensional structure space.  ...  Acknowledgements The authors would like to thank Gerhard Steger and his colleagues at the Institute for Physical Biology, Heinrich-Heine University, Düsseldorf, for many stimulating discussions on structure  ... 
doi:10.1093/bioinformatics/15.1.32 pmid:10068690 fatcat:77aygl6gi5b7fdeks6z6t2qmfe

A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure

Sean R Eddy
2002 BMC Bioinformatics  
The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N3) in memory. This is only practical for small RNAs.  ...  Optimal ribosomal RNA structural alignments that previously required up to 150 GB of memory now require less than 270 MB.  ...  I also wish to thank Elena Rivas and Robin Dowell for critical comments on the manuscript.  ... 
pmid:12095421 pmcid:PMC119854 fatcat:j4zsregp5fgtzn4xbfyjcdya3a

RNA Secondary Structures [chapter]

Qijun He, Matthew Macauley, Robin Davies
2015 Algebraic and Discrete Mathematical Methods for Modern Biology  
In an RNA model, the position of hooks and loops would allow the ribbon to fold and attach to itself.  ...  The specific shape into which RNAs fold plays a major role in their function, which makes RNA folding of prime interest to scientists.  ...  to the folding algorithms.  ... 
doi:10.1016/b978-0-12-801213-0.00013-7 fatcat:yvbevotprvdnlbygw3qynsky3q

Statistical Analysis of RNA Backbone

E. Hershkovitz, G. Sapiro, A. Tannenbaum, L.D. Williams
2006 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
Adapting techniques from optimal quantization to the RNA structure, we find torsion angle clusters and RNA conformational motifs.  ...  Local conformation is an important determinant of RNA catalysis and binding.  ...  P), whereas an RNA suite goes from sugar to sugar (or base to base).  ... 
doi:10.1109/tcbb.2006.13 pmid:17048391 pmcid:PMC2811324 fatcat:mzczarmtk5hmrfk76gbt334yey

Matching and Significance Evaluation of Combined Sequence-Structure Motifs in RNA

Carsten Meyer, Robert Giegerich
2002 Zeitschrift fur physikalische Chemie (Munchen. 1991)  
motifs in RNA.  ...  The discipline of Algebraic Dynamic Programming is a powerful method to design and implement versatile pattern matching algorithms on sequences; here we consider mixed sequence and secondary structure  ...  Acknowledgement We thank Thomas Töller for providing informations about the IRE and the SECIS patterns as well as the sequences for testing our programms.  ... 
doi:10.1524/zpch.2002.216.2.193 fatcat:2iue37au4jfglmbz7gk67oekva

Computational Analysis of RNAs

S.R. EDDY
2006 Cold Spring Harbor Symposia on Quantitative Biology  
ACKNOWLEDGMENTS I am grateful to Elena Rivas, Ariane Machado-Lima, and Eric Nawrocki for comments on the manuscript.  ...  Algorithms well suited for RNA secondary structure and sequence analysis have been borrowed from computational linguistics.  ...  Just as all HMMs have a common parsing algorithm (the Viterbi algorithm), all SCFGs have a common parsing algorithm, the CYK algorithm.  ... 
doi:10.1101/sqb.2006.71.003 pmid:17381287 fatcat:vnjeokzptvdjfc7tgnj65hwgh4

pVACtools: a computational toolkit to identify and visualize cancer neoantigens [article]

Jasreet Hundal, Susanna Kiwala, Joshua McMichael, Christopher A Miller, Alexander T Wollam, Huiming Xia, Connor J Liu, Sidi Zhao, Yang-Yang Feng, Aaron P Graubert, Amber Z Wollam, Jonas Neichin (+6 others)
2018 bioRxiv   pre-print
We have developed an in silico sequence analysis method - pVACtools, to facilitate comprehensive neoantigen characterization.  ...  workflow consists of tools for neoantigen prediction from somatic alterations (pVACseq and pVACfuse), prioritization and selection using a graphical web-based interface (pVACviz), and determining the optimal  ...  We also thank our growing user community for testing the software and providing useful input, critical bug reports as well as suggestions for improvement and new features. We are grateful to Drs.  ... 
doi:10.1101/501817 fatcat:d7wyfeor2vburc7kh5qqzf5u3y

Bellman's GAP

Georg Sauthoff, Stefan Janssen, Robert Giegerich
2011 Proceedings of the 13th international ACM SIGPLAN symposium on Principles and practices of declarative programming - PPDP '11  
Dynamic programming is a well-established technique to solve combinatorial optimization problems.  ...  This article introduces the GAP-L language, demonstrates the benefits of developing dynamic programming algorithms in a declarative framework by educational example, and reports on the practice of programming  ...  An O(n 6 ) time, O(n 4 ) space algorithm To give an example for an algorithm of higher complexity, let us seek optimal joint palindrome structures for two sequences, as exemplified by MI-SSISSIPPI +( (  ... 
doi:10.1145/2003476.2003484 dblp:conf/ppdp/SauthoffJG11 fatcat:akbfykh2dzfhjjxebnjzrj5xd4

pVACtools: a computational toolkit to identify and visualize cancer neoantigens

Jasreet Hundal, Susanna Kiwala, Joshua McMichael, Christopher A Miller, Huiming Xia, Alexander T Wollam, Connor J Liu, Sidi Zhao, Yang-Yang Feng, Aaron P Graubert, Amber Z Wollam, Jonas Neichin (+6 others)
2020 Cancer immunology research  
Prediction of peptide:MHC binding is accomplished by supporting an ensemble of MHC Class I and II binding algorithms within a framework designed to facilitate the incorporation of additional algorithms  ...  We have built a computational framework called pVACtools that, when paired with a well-established genomics pipeline, produces an end-to-end solution for neoantigen characterization. pVACtools supports  ...  We also thank our growing user community for testing the software and providing useful input, critical bug reports, as well as suggestions for improvement and new features. We are grateful to Drs.  ... 
doi:10.1158/2326-6066.cir-19-0401 pmid:31907209 pmcid:PMC7056579 fatcat:calagavk6ratblx53givvw5olm

Ambivalent covariance models

Stefan Janssen, Robert Giegerich
2015 BMC Bioinformatics  
Results: We propose an extension to the fundamental architecture of covariance models to allow for several, compatible consensus structures.  ...  For example, some transfer-RNAs exhibit a fifth helix in addition to the typical cloverleaf structure.  ...  We also thank the anonymous reviewers, whose comments helped to significantly improve the manuscript.  ... 
doi:10.1186/s12859-015-0569-1 pmid:26017195 pmcid:PMC4504443 fatcat:oyvbhcwicncqjdzanwbdumfd4u

Evaluation of a sophisticated SCFG design for RNA secondary structure prediction

Markus E. Nebel, Anika Scheid
2011 Theory in biosciences  
Investigations on both the accuracies of predicted foldings and the overall quality of generated sample sets (especially on an abstraction level, called abstract shapes of generated structures, that is  ...  This SCFG actually serves as the foundation for a statistical sampling algorithm for RNA secondary structures of a single sequence that represents a probabilistic counterpart to the sampling extension  ...  Acknowledgements The authors wish to thank two anonymous reviewers for their careful and helpful remarks and suggestions made for a previous version of this article.  ... 
doi:10.1007/s12064-011-0139-7 pmid:22135038 fatcat:a7p4b62w4nedxewvuuranz5r2q
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