Filters








4,496 Hits in 4.5 sec

A partition function algorithm for interacting nucleic acid strands

Hamidreza Chitsaz, Raheleh Salari, S. Cenk Sahinalp, Rolf Backofen
2009 Computer applications in the biosciences : CABIOS  
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]

Hamidreza Chitsaz
2010 arXiv   pre-print
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

Joseph N. Zadeh, Conrad D. Steenberg, Justin S. Bois, Brian R. Wolfe, Marshall B. Pierce, Asif R. Khan, Robert M. Dirks, Niles A. Pierce
2010 Journal of Computational Chemistry  
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

Robert M. Dirks, Justin S. Bois, Joseph M. Schaeffer, Erik Winfree, Niles A. Pierce
2007 SIAM Review  
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

R. A. Forties, R. Bundschuh
2009 Bioinformatics  
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]

Hamidreza Chitsaz, Rolf Backofen, S. Cenk Sahinalp
2009 Lecture Notes in Computer Science  
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

Michael Zuker
2003 Genome Informatics Series  
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  
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

Jerzy Kozyra, Harold Fellermann, Ben Shirt-Ediss, Annunziata Lopiccolo, Natalio Krasnogor
2017 Proceedings of the Genetic and Evolutionary Computation Conference on - GECCO '17  
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

Russell P. Goodman
2005 BioTechniques  
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]

Roumen A. Dimitrov
2005 arXiv   pre-print
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

Keishi Suga, Hibiki Tomita, Seishiro Tanaka, Hiroshi Umakoshi
2012 International Journal of Biological Sciences  
(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

Hamidreza Chitsaz, Elmirasadat Forouzmand, Gholamreza Haffari
2013 Journal of Computational Biology  
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]

Hamidreza Chitsaz and Elmirasadat Forouzmand and Gholamreza Haffari
2013 arXiv   pre-print
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

Xiaojun Xu, Shi-Jie Chen, Xuhui Huang
2016 PLoS ONE  
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
« Previous Showing results 1 — 15 out of 4,496 results