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A partition function algorithm for interacting nucleic acid strands
2009
Computer applications in the biosciences : CABIOS
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We also present a corresponding dynamic programming algorithm that computes the partition function over (almost) all physically possible joint secondary structures formed by two interacting nucleic acids ...
Results: We present a model for analyzing the thermodynamics of two interacting nucleic acid strands considering the most general type of interactions studied in the literature. ...
to compute a partition function of two interacting nucleic acid strands. ...
doi:10.1093/bioinformatics/btp212
pmid:19478011
pmcid:PMC2687966
fatcat:ujc5eelr2nbw7ogsw4j4q76bze
Prediction of RNA-RNA interaction structure by centroids in the Boltzmann ensemble
[article]
2010
arXiv
pre-print
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Although there are algorithms to predict minimum free energy interaction secondary structure for two nucleic acids, little work has been done to exploit the information invested in the base pair probabilities ...
Our sampling algorithm uses a balanced scheme for traversing indices which improves the running time of the Ding-Lawrence sampling algorithm. ...
Also, recently powerful algorithms for computing the partition function of interacting nucleic acid strands have been given (see our previous work [10] , for example, or [20] ). ...
arXiv:1002.1736v1
fatcat:tw3to4gefzc6hg4x3adky6srei
NUPACK: Analysis and design of nucleic acid systems
2010
Journal of Computational Chemistry
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The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. ...
The NUPACK web server (http://www.nupack.org) currently enables: • Analysis: thermodynamic analysis of dilute solutions of interacting nucleic acid strands. • Design: sequence design for complexes of nucleic ...
of interacting nucleic acid strands in the absence of pseudoknots. ...
doi:10.1002/jcc.21596
pmid:20645303
fatcat:izrwy3b2u5b2hjfprkxlaebpxm
Thermodynamic Analysis of Interacting Nucleic Acid Strands
2007
SIAM Review
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We then derive the form of the partition function for a fixed volume containing a dilute solution of nucleic acid complexes. ...
Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic ...
Pierce for helpful discussions during the course of the work. ...
doi:10.1137/060651100
fatcat:iqo3vdebmnafpat7jc2sxrr6bu
Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure
2009
Bioinformatics
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Results: We develop a model for predicting nucleic acid secondary structure in the presence of single-stranded binding proteins, and implement it as an extension of the Vienna RNA Package. ...
Therefore, accurate modeling of the interaction between single-stranded nucleic acids and such proteins is essential to fully understand many biological processes. ...
ACKNOWLEDGEMENT We thank Paul Barbara for helpful discussions of the behavior of single-stranded binding proteins. Conflict of Interest: none declared. ...
doi:10.1093/bioinformatics/btp627
pmid:19889798
fatcat:6knzttbyabbx5msraprdl6vbve
biRNA: Fast RNA-RNA Binding Sites Prediction
[chapter]
2009
Lecture Notes in Computer Science
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We present biRNA, a novel algorithm for prediction of binding sites between two RNAs based on minimization of binding free energy. ...
Moreover, biRNA can handle crossing interactions as well as hairpins interacting in a zigzag fashion. ...
for a nucleic acid secondary structure [26] . ...
doi:10.1007/978-3-642-04241-6_3
fatcat:y6oytafqivbrjm6oaavktrh37i
Predicting Nucleic Acid Hybridization and Melting Profiles
2003
Genome Informatics Series
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Similarly, melting temperatures for folded, single stranded oligonucleotides, or hybridized pairs of single stranded nucleic acids are usually determined using simple two state models that assume a single ...
In addition, the accurate prediction of melting profiles between an oligonucleotide and a target nucleic acid is also of great value. ...
Ideas for further research will be discussed, including the consideration of base stacking in unfolded, single stranded nucleic acids. ...
doi:10.11234/gi1990.14.266
fatcat:t4bbgntv3jd7zob3o2qz3jnhhe
DESIGN OF POTENTIAL RNAi MOLECULES FOR TARGETING COVID-19
2020
International Journal of Biology Pharmacy and Allied Sciences
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Since the scale of this new disease is humongous a novel vaccine for the effective treatment of the infected patients is yet to be developed. ...
COVID 19 is a highly communicable disease caused by a subfamily of a coronavirinae specifically known as SARS CoV-2 of beta coronavirus family. ...
function of melting
temperature (Tm) for a hybridized nucleic
9. ...
doi:10.31032/ijbpas/2020/9.11.5245
fatcat:2o7tlpdykrfgdndwt3gjl5jrye
Optimizing nucleic acid sequences for a molecular data recorder
2017
Proceedings of the Genetic and Evolutionary Computation Conference on - GECCO '17
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We envision that this approach can be generalized towards a broad class of toehold-mediated strand displacement systems. . 2017. Optimizing nucleic acid sequences for a molecular data recorder. In ...
Here we present an evolutionary algorithm tailored to optimising nucleic acid sequences that predictively fold into our desired target structures. ...
genetic algorithm to generate nucleic acid sequences that optimize the functioning of a DNA nano-device, namely a molecular signal recorder. ...
doi:10.1145/3071178.3071345
dblp:conf/gecco/KozyraFSLK17
fatcat:7atuyoavzzh7vmwp3kgsae4pqu
NANEV: a program employing evolutionary methods for the design of nucleic acid nanostructures
2005
BioTechniques
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A partition function algorithm for nucleic acid secondary structure including pseudoknots. J. Comput. Chem. 24:1664-1677. 13. McCaskill, J.S. 1990. ...
The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29:1105-1119. ...
doi:10.2144/05384bm06
pmid:15884672
fatcat:rl5rsncue5aalnruh6bnmuwy4y
A new formalism for calculation of the partition function of single stranded nucleic acids
[article]
2005
arXiv
pre-print
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A new formalism for calculation of the partition function of single stranded nucleic acids is presented. ...
Calculations on short and long sequences show, that for short oligonucleotides, a duplex formation often displays a two-state transition. ...
Based on the multiplication property of the partition function, here we present a new formalism for calculation of the partition function of a single stranded nucleic acids. ...
arXiv:q-bio/0510011v1
fatcat:6nkj735v7jhdpc46gqjwwjjuky
Hydrophobic Properties of tRNA with Varied Conformations Evaluated by an Aqueous Two-Phase System
2012
International Journal of Biological Sciences
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(LH) were evaluated based on the partition coefficient of tRNA in the ATPS. ...
The HFS value of the DNA duplex was found to be hydrophilic, compared to that of the single-stranded DNA, indicating that the exposure of nucleobases is a key factor of the hydrophobic properties of nucleotides ...
This work was supported by the Funding Program for Next Generation World-Leading Researchers of the Council for Science and Technology Policy (CSTP) (GR066), and a grant from the Global COE program "Bio-Environmental ...
doi:10.7150/ijbs.5059
pmid:23091416
pmcid:PMC3477688
fatcat:hzszsemwrvafra3772losqvpgq
An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids
2013
Journal of Computational Biology
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Our goal in this paper is to give a fast algorithm, based on sparse folding, to calculate an upper bound on the partition function. ...
For instance, the space complexity of the partition function for RNA-RNA interaction is O(n 4 ) and the time complexity is O(n 6 ) which are prohibitively large [4, 12] . ...
Conclusion We gave a fast algorithm, based on the recent algorithm of Hazan and Jaakkola [10] , to iteratively compute an upper bound on the partition function of nucleic acids by perturbing energy. ...
doi:10.1089/cmb.2013.0003
pmid:23829650
fatcat:emvrvcrkirckbkflbrr3dpreay
An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids
[article]
2013
arXiv
pre-print
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Our goal in this paper is to give a fast algorithm, based on sparse folding, to calculate an upper bound on the partition function. ...
For instance, the space complexity of the partition function for RNA-RNA interaction is O(n^4) and the time complexity is O(n^6) which are prohibitively large [4,12]. ...
Conclusion We gave a fast algorithm, based on the recent algorithm of Hazan and Jaakkola [10] , to iteratively compute an upper bound on the partition function of nucleic acids by perturbing energy. ...
arXiv:1301.1590v1
fatcat:qc6rdylds5fv7lkvbw7r5dqymi
VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability
2016
PLoS ONE
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Based on a partition function-based algorithm, the server enables prediction for structure with and without tertiary contacts. ...
RNA-RNA interactions are essential for genomic RNA dimerization, mRNA splicing, and many RNA-related gene expression and regulation processes. ...
NUPACK [12] extends the single-stranded partition function algorithm to treat multiple interacting nucleic acid strands with a dynamic programming algorithm. ...
doi:10.1371/journal.pone.0163454
pmid:27657918
pmcid:PMC5033388
fatcat:rncjaiswefddtjnixkxow4e6wm
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