RNA structure
Characteristics of equipartition for RNA structure
... from RNA STRAND, validated by NMR or X-Ray. For most RNA sequences, the length of multiple domains is close to ...of RNA from a new angle, which is more close to natural ...long RNA ...
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Advances in RNA Structure Prediction from Sequence: New Tools for Generating Hypotheses about Viral RNA Structure-Function Relationships
... of RNA structure pre- diction by free-energy minimization ...about RNA structure and ...ferent RNA structure prediction programs have been reviewed elsewhere (26, 42, ...an ...
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Influenza B virus has global ordered RNA structure in (+) and (−) strands but relatively less stable predicted RNA folding free energy than allowed by the encoded protein sequence
... indicates that wild-type sequences in the (+)RNA sense generally have less stable secondary structure than sequences with codon mutants (Table 1). Only NP breaks this trend, where the in silico ...
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DotAligner: identification and clustering of RNA structure motifs
... homologous RNA structures from a large set of query ...pairwise RNA structure align- ment algorithms through several iterations of a stochas- tic sampling strategy across all Rfam seed alignments, ...
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Sparsification of RNA structure prediction including pseudoknots
... The presented work gives four examples for sparsifica- tion in the context of gap fragments and a complex recursion structure. We successfully sparsified the fast- est and the most complex pseudo-knot ...
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Analysis of Rnase P RNA Structure and Function
... stabilizing RNA structure, enhancing affinity of bound substrate, and increasing ...the RNA, which suggests a greater involvement in structural stabilization than previously thought ...
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Global RNA Structure Analysis of Poliovirus Identifies a Conserved RNA Structure Involved in Viral Replication and Infectivity
... single-stranded RNA genome of positive ...the RNA genome ...the RNA. The 5= UTR contains a structure critical for viral translation (the internal ribosome entry site or IRES) (3, 4), as well ...
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Bioinformatic and Physical Characterizations of Genome-Scale Ordered RNA Structure in Mammalian RNA Viruses
... large-scale RNA structure and host persistence. The RNA secondary structure, calculated as the probability of the internal base pairing of individual bases in an RNA molecule, has been ...
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Torus principal component analysis with applications to RNA structure
... to RNA structure analysis we provide for a novel dimension reduction method at residue level and we apply it within the focus of current research to single residue ...large RNA data set carefully ...
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RNA structure and heterologous recombination in the double-stranded RNA bacteriophage phi 6.
... coli lacZAm15 amp PT7 PT3 lacZ' amp lacZ' kan cartridge in PstI site Cartridge with most of lacZ amp lacZ' with pUC8 MCS; vector for pseudomonads amp PT7; exact copy of segment M in pT7T[r] ...
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Methods for high-throughput analysis of RNA structure and dynamics
... 5.4.4 Primer Extension and Data Analysis of Modified RNA. The general procedure was that outlined previously [30]. Briefly, a fluorescently labeled DNA primer was annealed to the RNA (10 µL, from the ...
137
Changes in RNA secondary structure affect NS1 protein expression during early stage influenza virus infection
... We next determined whether these RNA structure dif- ferences are involved in viral replication. We rescued 4 influenza viruses that have predicted combinations of NS gene RNA secondary structures. ...
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Base specific spin labeling of RNA for structure determination
... the structure and conformational dynamics of these RNA systems ...the RNA structure and ...two RNA forms are correlated, indicating that the structure simultaneously moves away ...
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Structure of noncoding RNA is a determinant of function of RNA binding proteins in transcriptional regulation
... of RNA into divergent structures is constrained by specific RNA sequences under physiological condi- ...sequence-and structure- specific manners, mimicking an open promoter struc- tures and ...
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Comparative Analysis of RNase P
... The Branhamella catarrhalis RNase P RNA was derived by comparison to the Haemophilus influenza RNase P RNA (Figure 2B). The helices are similar in length, but vary in sequence. This is typical for most ...
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Biology_Honors_Thesis_Submit.pdf
... these RNA secondary structures have on viral replication, we made mutations using an infectious clone ...stable RNA secondary structures in the viral RNA, to disrupt the RNA ...desired ...
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Prediction of RNA 3D Structure
... — RNA structures are generally organized hierarchically ...of RNA structure is a big challenge for the ...for RNA secondary structure ...tertiary structure is still a big area of ...
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The SHAPE of tRNA folding and of the 5'-end of the HIV-1 genome
... an RNA. Despite well documented exceptions, 4-6 current models for RNA folding and for de novo prediction of RNA structure emphasize that RNA folding is strongly ...secondary ...
127
Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE
... secondary structure alignments, they are not specifically designed to take advantage of the secondary structure ...to RNA structure logos [12] and 3D sequence logos of RNA alignments ...
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A Polyamide Inhibits Replication of Vesicular Stomatitis Virus by Targeting RNA in the Nucleocapsid
... structured RNA bound in the nucleo- capsid of a negative-strand RNA ...genomic RNA encapsidated in the nucleocapsid forms a structure resembling one strand of an A-form RNA ...
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