RNA secondary structure
SP fold – Speculative Parallelization for Parallel Algorithm of RNA Secondary Structure Prediction on Multicore
... RNA secondary structure prediction is the problem of determining the most stable structure for a given ...the structure. Thus we want to find a structure of minimal free energy ...
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Novel polybasic cleavage site in SARS-CoV-2 genome is likely to induce a major change in the RNA secondary structure
... local RNA secondary structure predictions for WT and DM in an extended region around the 12-base ...the structure estimated for S0 (shown in red in Figure 2E) is identical in both locally ...
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Research on folding diversity in statistical learning methods for RNA secondary structure prediction
... of RNA folding rules is confirmed by dimension reduction and cluster analysis, and the relationship between folding rules and family is also ...the RNA function in the same ...an RNA with an unknown ...
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Importance of the Positive-Strand RNA Secondary Structure of a Murine Coronavirus Defective Interfering RNA Internal Replication Signal in Positive-Strand RNA Synthesis
... single-strand RNA bacteriophage Qb contains two internal viral polymerase rec- ognition sites for negative-strand RNA synthesis; each internal recognition site is separated from its functional initiation ...
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Prediction of RNA Secondary Structure from Random Sequences using ZEM
... a secondary structure, each base has at most one ...lollipop-shaped structure is a key building block of many RNA secondary ...the structure, the loop is called a bulge ...the ...
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Accelerating calculations of RNA secondary structure partition functions using GPUs
... Figure 1 shows the root-mean-square deviation (RMSD) between base-pair probabilities calculated using double precision and either single precision, or the modified parameters. The RMSD of the calculation using modi- fied ...
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Characterization of an Essential RNA Secondary Structure in the 3′ Untranslated Region of the Murine Coronavirus Genome
... targeted RNA recombination (20, 22, 31, 40, ...via RNA-RNA recombina- tion between a synthetic donor RNA and the genome of a recipient virus that can be selected ...targeted RNA ...
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Genome-Wide Approaches To Study Rna Secondary Structure
... just RNA expression, but several other aspects of RNA ...of RNA biology: RNA-secondary structure, RNA cleavage, and regulatory small ...determining RNA ...
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GTfold: Enabling parallel RNA secondary structure prediction on multi core desktops
... We also demonstrate that GTfold’s reduced running time does not come at the expense of prediction accuracy, rel- ative to UNAfold and RNAfold, as measured against ribo- somal structures obtained by comparative sequence ...
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Changes in RNA secondary structure affect NS1 protein expression during early stage influenza virus infection
... RNA secondary structures play a key role in splicing, gene expression, microRNA biogenesis, RNA editing, and other biological ...of RNA structures has been demonstrated in the life cycle of ...
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Reconstructing phylogeny from RNA secondary structure via simulated evolution
... the structure metric we used, and, second, that at some (limited) parameter values, our structure metric appears to out-perform some of the sequence-based metrics (Figure 6); to answer any of these ...
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Thermal adaptation of the phage G4 and molecular evolution of RNA secondary structure
... Following Kimura (1985), we consider the substitution process at a pair of loci involved in a compensatory interaction in a diploid population of size N (equivalent results are obtained for a haploid population of size 2 ...
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Ebola Virus VP30-Mediated Transcription Is Regulated by RNA Secondary Structure Formation
... minigenomic RNA and nucleocapsid proteins ...minigenomic RNA is un- affected by VP30, whereas transcription is strongly dependent on the presence of VP30 ...species, RNA purifica- tion was performed ...
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Genome-Wide Analysis of RNA Secondary Structure in Eukaryotes
... global structure-sensitive assays (dsRNA- and ssRNA- seq) and the tools to infer secondary structure from these data ...input RNA, extent of RNase treatment, ...varied RNA population ...
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The 5' nontranslated region of hepatitis A virus RNA: secondary structure and elements required for translation in vitro.
... Nucleotide substitutions in specific virus strains from the wild-type HM175 sequence are shown in boldface type; base pairs identified by covariant substitutions among all nine strains a[r] ...
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A retroviral RNA secondary structure required for efficient initiation of reverse transcription.
... Second, U5 deletion and leader substitution mutations which would disrupt the U5-leader stem structure in ATVA6, ATVA15, ATVA21, and ATVAL resulted in a decrease in the efficiency of vir[r] ...
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5-Azacytidine and RNA secondary structure increase the retrovirus mutation rate.
... b The first number indicates the number of different mutations obtained, while the second number indicates the total number of proviruses recovered with the type of mutation indicated.. [r] ...
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Development of Interest in Science and Interest in Teaching Elementary Science: Influence of Informal, School, and Inquiry Methods Course Experiences
... prevalent RNA structures. It is widely recognized that RNA secondary structures play an important role in RNA ...between RNA secondary structures and RNA pseudoknots using ...
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RNA Structures Facilitate Recombination-Mediated Gene Swapping in HIV-1
... of RNA structure, inferred statistically, was further investigated by mapping recombina- tion rates onto the experimentally constrained HIV-1 env sec- ondary structure for the NL4-3 genome ...the ...
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Random generation of RNA secondary structures according to native distributions
... of RNA secondary structures according to an ela- borate and thus very realistic ...considered RNA secondary structures as realistic as possible, distinguishes between all known structural ...
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