Thermodynamic and phylogenetic prediction of RNA - NCBI
The existence and functional importance of RNA secondary structure in the ... of hepatitis C virus (HCV), including thermodynamic prediction, calculation of ..... plotted against genome position (Fig+ 7)+ The greatest ... Parallel testing of native sequences in reverse, .... and 39 untranslated regions, little progress has been.
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Knowledge Discovery in RNA Sequence Families of HIV - CiteSeerX
... structure prediction algo- rithm for hypercube-type parallel computers al- ... plete RNA virus genomes such as HIV-1 and ... prediction of RNA secondary structure from sequence .... and describe the progress we have made towards the .
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bridgin the gas in RNA structure prediction.pdf - RNA Informatics
Mar 23, 2007 ... The field of RNA structure prediction has experienced significant ... determine RNA secondary structures and pseudoknots from sequence.
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Knowledge Discovery in RNA Sequence Families of HIV Using
prediction of RNA secondary structure from sequence information is based upon ... parallel machines enable not just the prediction of sec- ondary structure for ...
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Sequence–structure relationships in yeast mRNAs - Nucleic Acids
Sep 27, 2011 ... RNA molecules sequence–structure relationships are relatively ... There is a selective pressure toward maintaining both ... Significant progress has been made in predicting RNA ... structures using the novel technology called parallel ..... secondary structural elements for the expression of influenza virus.
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Exploring the RNA Folding Energy Landscape Using Scalable
Jun 25, 2010 ... considerable interest towards the prediction of RNA fold- ... of Bovine Corona Virus, Runtime Environment, Distributed .... including high-throughput of highly- parallel tasks, many ... vances in cyberinfrastructure to make progress towards the ... The probability of a secondary structure, Ii, of a sequence,.
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Current and Emerging Themes in the Structural Analysis of Viral
Sep 18, 2015 ... Viral RNA Genomes: Applications for the Development of Novel. Therapeutic ... structure. It will also examine the progress toward the ... or RNA sequence, is widely used for covariation analysis of ... softwares for predicting secondary structures from ... then prepared for massive parallel sequencing. Hence ...
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Tertiary Motifs in RNA Structure and Folding - Jennifer Doudna
primary sequence the RNA must be purified from its native source and ... uncertainty, is to use secondary structure prediction programs ... Progress has been made possible by improve- ... the hepatitis delta virus ribozyme) it is ... packed against one another. .... helices are oriented parallel with respect to one another. In.
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Multiscale Modeling of RNA Structure and Dynamics - CiteSeerX
significant progress has been made toward ab initio modeling of RNA 3D structures. 54 ... show that starting only with sequence, it is possible to predict the structures of some. 56 ..... or replicas of the same system are performed in parallel at different ... trajectory of one of the replicas for a turnip yellow mosaic virus (TYMV).
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Predicting and Modeling RNA Architecture - Cold Spring Harbor
May 24, 2010 ... tools allows for sequence and structure analysis as well as interactive modeling by ... which can be coupled or used in parallel. ... Since then, striking progress has occurred in. RNA .... mathematically based prediction of RNA structure at the ..... been applied to the cricket paralysis virus IRES RNA bound.
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Structural Differentiation of the HIV-1 Poly(A) Signals - JBSD taken
multiple HIV-1 strains using the Massively Parallel Genetic Algorithm (MPGAfold) capable of dynamically ... All HIV-1 viral RNA sequences contain a repetitive region at .... It is capable of predicting RNA secondary structure folding dynamics ..... progress through different states: a multibranch structure to a linear structure with.
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Computational approaches to RNA structure prediction, analysis
protein folding, much progress has been achieved in the past ... generation of RNA sequence pools for aptamer design. .... RNA structure prediction, analysis, and design Laing and Schlick 3 ..... folding funnel (base pair difference against free energy plotted for the .... hepatitis delta virus RNA, 5S, 16S, 23S rRNAs). Inspired ...
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Prediction of Geometrically Feasible Three Dimensional Structures
Oct 28, 2009 ... Keywords: RNA structure prediction, Pseudoknots, RNA free energy estimation ... related RNA sequences, thus is not always feasible. ... However, the lack of progress in calculating free energies ..... The approach of pk3D towards secondary structure ... nal of the moloney murine leukemia virus (PDB 1S9S).
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Structural analysis of the spiroplasma virus, SpV4 - Dr. Timothy S
Background: Spiroplasma virus, SpV4, is a small, non-enveloped virus that ... antiparallel β-barrel. Secondary structure prediction of this insertion sequence ... pointed towards the fivefold axes (Figure 2). The β ...... Progress in protein structure prediction. ... animal virus and its implication for membrane translocation of RNA.
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Progress Towards in Vivo Use of siRNAs
Feb 14, 2006 ... small interfering RNAs (siRNAs) as therapeutic agents, especially in the .... sequence enables sequence-specific targeting of this oth- ... synthesized and the problems surrounding its use parallel ... introduced into animals using plasmid or viral vectors. .... chemically synthesized RNA of known structure and.
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Structure and functionality in flavivirus NS-proteins: Perspectives for
Besides yellow fever virus, a landmark case in the history of viro. ... there has been a growing interest in discovering drugs against DENV and WNV. ... The 5′ -end of the (+)ssRNA genome is decorated by a RNA cap structure .... In parallel, studies of partial sequences commenced, focusing mainly on flavivirus E genes.
[ 1-s2.0-S0166354209005385-main.pdf?_tid=a96f8a06b5c5fc911ebfaaca1af141d0&acdnat=1334989159_7467987ca407a23bc93c08845ffa1266 - Read/Download File
Protein structure prediction from sequence variation
Nov 8, 2012 ... Substantial progress has recently been made on this problem ... results from massively parallel sequencing technology. ... A substantial step forward in protein -structure prediction is now on ..... A search of predicted structures against ... the realization, not unlike that for RNA structures but less obvious, that ...
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Patterns of Oligonucleotide Sequences in Viral and Host Cell RNA
these selection forces acting in parallel on both host innate immune genes and ssRNA viral genomes. We do this ... sequence motifs for reasons that are not functional or structural, one may ... of coding sequence (CDS) regions in human and chicken mRNA. ... against the background of the whole mouse genome, one can.
[ journal.pone.0005969.PDF - Read/Download File
Ab initio protein structure prediction, 216–217 amino acids (AAs
725 clinical decision, 725 human immunodeficiency virus, 725 ... pairwise sequence alignment, 1083. BLAST, 1083 .... protein structures, prediction, 789 .... related to RNA data analysis, 685 .... parallel k-mer distance computation, 1010,. 1011 ..... toward qualitative modeling of, 291 .... genome sequencing, progress, 1028.
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Structural Basis for Host Membrane Remodeling Induced by Protein
Oct 2, 2014 ... The complexity of viral RNA synthesis and the numerous participating ... five- stranded antiparallel ß-sheet that displays striking structural similarity to the ... domain of the 2B protein of hepatitis A virus (HAV). .... proteins and shares little, if any, sequence and structural similarity ... In particular, progress in the.
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