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Sorin Istrail, Pavel Pevzner, Ron Shamir
2000 Discrete Applied Mathematics  
Vingron proposes a new polyhedral approach to the classical sequence alignment problem.  ...  DNA sequence analysis: The paper "A Polyhedral approach to sequence alignment problem" by J.D. Kececioglu, H.P. Lenhof, K. Melhorn, P. Mutzel, K. Reinert and M.  ...  The paper "A uniÿed approach to word occurrence probabilities" by M. Regnier is related to algorithms for pattern (signal) discovery in DNA.  ... 
doi:10.1016/s0166-218x(00)00255-9 fatcat:cbst4oy6iveubnmwlas5x255r4

Geometric combinatorics and computational molecular biology: branching polytopes for RNA sequences [article]

Elizabeth Drellich, Andrew Gainer-Dewar, Heather A. Harrington, Qijun He, Christine Heitsch, Svetlana Poznanović
2016 arXiv   pre-print
secondary structure prediction for real RNA sequences.  ...  Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction.  ...  The DNA sequence alignment problem is to find the best alignment between sequences given some scoring function [35] .  ... 
arXiv:1509.04090v2 fatcat:7ukj5szfsndblmzyt2xoyobzwq

A polyhedral approach to sequence alignment problems

John D. Kececioglu, Hans-Peter Lenhof, Kurt Mehlhorn, Petra Mutzel, Knut Reinert, Martin Vingron
2000 Discrete Applied Mathematics  
The RNA sequence alignment problem captures the comparison of RNA molecules on the basis of their primary sequence and their secondary structure.  ...  Moreover, for multiple sequences the branch-and-cut algorithms for both sequence alignment problems are able to solve to optimality instances that are beyond the range of present dynamic programming approaches  ...  Acknowledgements The authors would like to thank Pavel Pevzner for pointing out an alternative proof to Lemma 15.  ... 
doi:10.1016/s0166-218x(00)00194-3 fatcat:bfrvjn5qjvbopkvb65wrygssq4


2000 Discrete Applied Mathematics  
Vingron, A polyhedral approach to sequence alignment problems (1}3) 143}186 King, J., see B. Berger (1}3) 97}111 Lenhof, H.-P., see J.D. Kececioglu (1}3) 143}186 Li, M., see L.  ...  ., A uni"ed approach to word occurrence probabilities (1}3) 259}280 SchaK !er, A.A., see R  ... 
doi:10.1016/s0166-218x(00)00254-7 fatcat:3a6jldvltvhmxaocekw4ykp2iq

Asymmetric Genome Organization in an RNA Virus Revealed via Graph-Theoretical Analysis of Tomographic Data

James A. Geraets, Eric C. Dykeman, Peter G. Stockley, Neil A. Ranson, Reidun Twarock, Claus O. Wilke
2015 PLoS Computational Biology  
Motivated by the important, cooperative roles of viral genomes in the assembly of single-stranded RNA viruses, we have developed a new analysis method that reveals the asymmetric structural organization  ...  By contrast, structure determination of asymmetric components remains a challenge, and novel analysis methods are required to reveal such features and characterize their functional roles during infection  ...  The resulting map for the outer RNA shell in the icosahedrally-averaged map was aligned with that for the asymmetric RNA organization in the tomogram by reference to the X-ray protein structure used to  ... 
doi:10.1371/journal.pcbi.1004146 pmid:25793998 pmcid:PMC4368512 fatcat:pd7mxwk25zhlhbjbgdiupvnc3a

Page 6831 of Mathematical Reviews Vol. , Issue 2001I [page]

2001 Mathematical Reviews  
polyhedral approach to sequence alignment problems.  ...  The RNA sequence alignment problem captures the comparison of RNA molecules on the basis of their primary sequence and their secondary structure.  ... 

Tiling Nussinov's RNA folding loop nest with a space-time approach

Marek Palkowski, Wlodzimierz Bielecki
2019 BMC Bioinformatics  
., one segment of an RNA sequence might be paired with another segment of the same RNA sequence into a two-dimensional structure composed by a list of complementary base pairs, which are close together  ...  An RNA primary structure, or sequence, is a single strand considered as a chain of nucleotides from the alphabet AUGC (adenine, uracil, guanine, cytosine).  ...  program for a prepared sequence in the FASTA format and obtain a target Nussinov table.  ... 
doi:10.1186/s12859-019-2785-6 fatcat:lu47i4i355abpmfxyoaojasjvi

Algorithmic design of 3D wireframe RNA polyhedra [article]

Antti Elonen, Ashwin K. Natarajan, Ibuki Kawamata, Lukas Oesinghaus, Abdulmelik Mohammed, Jani Seitsonen, Yuki Suzuki, Friedrich C. Simmel, Anton Kuzyk, Pekka Orponen
2022 bioRxiv   pre-print
As its output, the pipeline produces an RNA nucleotide sequence whose corresponding RNA primary structure can be transcribed from a DNA template and folded in the laboratory.  ...  Towards this goal, we introduce a general algorithmic design process and software pipeline for rendering 3D wireframe polyhedral nanostructures in single-stranded RNA.  ...  (21) introduced the complementary approach of RNA origami, wherein a single long RNA strand is folded directly into a structure that conforms to a prescribed design.  ... 
doi:10.1101/2022.04.27.489653 fatcat:cmiojx6drzedjicrdo2vi2owd4

Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing

Marek Palkowski, Wlodzimierz Bielecki
2017 BMC Bioinformatics  
RNA secondary structure prediction is a compute intensive task that lies at the core of several search algorithms in bioinformatics.  ...  Results: The purpose of this paper is to present a novel approach allowing for generation of a parallel tiled Nussinov RNA loop nest exposing significantly higher performance than that of known related  ...  Ethics approval and consent to participate Not applicable Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.  ... 
doi:10.1186/s12859-017-1707-8 pmid:28578661 pmcid:PMC5457642 fatcat:3mkuzqhsmrfqbp47d24dz62eua

Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence

Arpith C. Jacob, Jeremy D. Buhler, Roger D. Chamberlain
2010 2010 18th IEEE Annual International Symposium on Field-Programmable Custom Computing Machines  
We conclude with a number of lessons in using FPGAs to implement arrays after polyhedral analysis.  ...  We use a technique of Lyngsø to rewrite the recurrence in a form that makes polyhedral analysis more effective and use data pipelining and tiling to generate a hardware-friendly implementation.  ...  Chamberlain is a principal in BECS Technology, Inc.  ... 
doi:10.1109/fccm.2010.22 dblp:conf/fccm/JacobBC10 fatcat:kyzf3d7wtjdahgmxvyv5ggxw3m

Hierarchical self-assembly of complex polyhedral microcontainers

David J Filipiak, Anum Azam, Timothy G Leong, David H Gracias
2009 Journal of Micromechanics and Microengineering  
The concept of self-assembly of a two-dimensional (2D) template to a three-dimensional (3D) structure has been suggested as a strategy to enable highly parallel fabrication of complex, patterned microstructures  ...  It is a highly effective way to massproduce patterned, complex 3D structures on the microscale and could also facilitate encapsulation of cargo in a parallel and cost-effective manner.  ...  Thus, a good methodology to fabricate such higher-order polyhedral structures is needed.  ... 
doi:10.1088/0960-1317/19/7/075012 pmid:20161118 pmcid:PMC2740998 fatcat:maftq5dxwjbgvhwe2rbyewg6bi

Parametric Analysis of RNA Branching Configurations

Valerie Hower, Christine E. Heitsch
2011 Bulletin of Mathematical Biology  
We additionally map a collection of known RNA secondary structures to the RNA polytope.  ...  A vertex of this polytope corresponds to RNA secondary structures with common branching.  ...  There is also earlier polyhedral work on parametric sequence alignment (Gusfield et al. 1992; Waterman et al. 1992 ) and related work on secondary structure comparison (Wang and Zhao 2003) and sequence  ... 
doi:10.1007/s11538-010-9607-3 pmid:21207176 fatcat:ruxbybk26vg35cxhyehxfkm24e

Molecular systematics of Barbatosphaeria (Sordariomycetes): multigene phylogeny and secondary ITS structure

M. Réblová, K. Réblová, V. Štěpánek
2015 Persoonia  
A dichotomous key to species accepted in the genus is provided.  ...  The genus is expanded to encompass nine species with both septate and non-septate ascospores in clavate, stipitate asci with a non-amyloid apical annulus and non-stromatic ascomata with a long decumbent  ...  and relies on multiple sequence alignment of related RNA sequences.  ... 
doi:10.3767/003158515x687434 pmid:26823626 pmcid:PMC4713105 fatcat:knlhoijpwfafjoccvlvho6b7ue

Advances in the Bioinformatics Knowledge of mRNA Polyadenylation in Baculovirus Genes

Iván Gabriel Peros, Carolina Susana Cerrudo, Marcela Gabriela Pilloff, Mariano Nicolás Belaich, Mario Enrique Lozano, Pablo Daniel Ghiringhelli
2020 Viruses  
involves bibliography information, data mining, RNA structure and a comprehensive study of the core gene 3′ ends from 180 baculovirus genomes.  ...  recombinant proteins or the gene delivery of therapeutic sequences in mammals, among others.  ...  72]AlignmentsClustal software for multiple sequence alignment which algorithm proceeds in a three-steps-routine, including pairwise alignment, distance matrix determination and guide tree creation to align  ... 
doi:10.3390/v12121395 pmid:33291215 fatcat:cp2j46psmfdwdmy7423epq5kvu

Page 2126 of Mathematical Reviews Vol. , Issue 2001C [page]

2001 Mathematical Reviews  
Kececioglu, Hans-Peter Lenhof, Kurt Mehlhorn, Petra Mutzel, Knut Reinert and Martin Vingron, A polyhedral approach to sequence alignment problems (143-186); Brendan Mumey, Probe location in the presence  ...  Hwa, An analytic study of the phase transition line in local sequence alignment with gaps (113-142); John D.  ... 
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