A comparative method for finding and folding RNA secondary structures within protein-coding regions - sprookjes - yvandenbroek - TriplyDB

A comparative method for finding and folding RNA secondary structures within protein-coding regions

A comparative method for finding and folding RNA secondary structures within protein-coding regions

http://www.wikidata.org/entity/Q37537881

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Identification and classification of conserved RNA secondary structures in the human genome XRate: a fast prototyping, training and annotation tool for phylo-grammars SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework Architecture and secondary structure of an entire HIV-1 RNA genome Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.Identification of potential conserved RNA secondary structure throughout influenza A coding regions Evidence of a novel RNA secondary structure in the coding region of HIV-1 pol gene Structured RNAs in the ENCODE selected regions of the human genome Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs.Multiple sequence alignments of partially coding nucleic acid sequences.Studying Hepatitis C Virus: Making the Best of a Bad Virus Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses A Hepatitis C Virus cis-Acting Replication Element Forms a Long-Range RNA-RNA Interaction with Upstream RNA Sequences in NS5B Compensatory Evolution in RNA Secondary Structures Increases Substitution Rate Variation among Sites From consensus structure prediction to RNA gene finding Bioinformatics of prokaryotic RNAs LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search e-RNA: a collection of web servers for comparative RNA structure prediction and visualisation.ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction.Conserved secondary structures in Aspergillus.Evolutionary modeling and prediction of non-coding RNAs in Drosophila TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures Developing and applying heterogeneous phylogenetic models with XRate.Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and non-conserved structural motifs.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.Strong epistatic selection on the RNA secondary structure of HIV Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes.In silico discovery and modeling of non-coding RNA structure in viruses.xREI: a phylo-grammar visualization webserver.Number variation of high stability regions is correlated with gene functions.Transient RNA structure features are evolutionarily conserved and can be computationally predicted.The effect of gene overlapping on the rate of RNA virus evolution Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis.Identification of conserved RNA secondary structures at influenza B and C splice sites reveals similarities and differences between influenza A, B, and C.On the importance of cotranscriptional RNA structure formation The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective.Random generation of RNA secondary structures according to native distributions.Solving the master equation for Indels.On the origin of synonymous codon usage divergence between thermophilic and mesophilic prokaryotes.Comparative RNA Genomics.

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A comparative method for finding and folding RNA secondary structures within protein-coding regions

http://www.wikidata.org/entity/Q37537881

description

article científic

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article scientifique

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articolo scientifico

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artigo científico

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bilimsel makale

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scientific article published on 24 September 2004

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vedecký článok

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vetenskaplig artikel

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videnskabelig artikel

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vědecký článek

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name

A comparative method for findi ...... within protein-coding regions

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A comparative method for findi ...... within protein-coding regions.

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type

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A comparative method for findi ...... within protein-coding regions

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A comparative method for findi ...... within protein-coding regions.

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A comparative method for findi ...... within protein-coding regions

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A comparative method for findi ...... within protein-coding regions.

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Nucleic Acids Research

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A comparative method for findi ...... within protein-coding regions

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Irmtraud Margret Meyer

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Jotun Hein

http://www.w3.org/2001/XMLSchema#string

Peter Simmonds

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Roald Forsberg

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P2860

Non–coding RNA genes and the modern RNA world

Mfold web server for nucleic acid folding and hybridization prediction

Structure-function analysis of the 3' stem-loop of hepatitis C virus genomic RNA and its role in viral RNA replication

Noncoding RNA gene detection using comparative sequence analysis

An evolutionarily conserved RNA stem-loop functions as a sensor that directs feedback regulation of RNase E gene expression

RNA sequence analysis using covariance models

A cis-acting replication element in the sequence encoding the NS5B RNA-dependent RNA polymerase is required for hepatitis C virus RNA replication

Pfold: RNA secondary structure prediction using stochastic context-free grammars

Internal initiation of translation of hepatitis C virus RNA: the ribosome entry site is at the authentic initiation codon.

Thermodynamic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus

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4925-4936

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scholarly article

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10.1093/NAR/GKH839

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16

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32

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Jakob Skou Pedersen

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2004-09-24T00:00:00Z

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8267410

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15448187

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protein structure

protein folding

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519121

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