Cargando…

RNA structure prediction from evolutionary patterns of nucleotide composition

Structural elements in RNA molecules have a distinct nucleotide composition, which changes gradually over evolutionary time. We discovered certain features of these compositional patterns that are shared between all RNA families. Based on this information, we developed a structure prediction method...

Descripción completa

Detalles Bibliográficos
Autores principales:	Smit, S., Knight, R., Heringa, J.
Formato:	Texto
Lenguaje:	English
Publicado:	Oxford University Press 2009
Materias:	Computational Biology
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655677/ https://www.ncbi.nlm.nih.gov/pubmed/19129237 http://dx.doi.org/10.1093/nar/gkn987

Ejemplares similares

Evolutionary rates vary among rRNA structural elements
por: Smit, S., et al.
Publicado: (2007)

Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide–nucleotide interactions from direct coupling analysis
por: Wang, Jian, et al.
Publicado: (2017)

Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides
por: Hopfinger, Melissa C, et al.
Publicado: (2020)

Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters
por: Dey, Sucharita, et al.
Publicado: (2012)

Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures
por: Cao, Jingyi, et al.
Publicado: (2021)

An evolutionary conserved pattern of 18S rRNA sequence complementarity to mRNA 5′ UTRs and its implications for eukaryotic gene translation regulation
por: Pánek, Josef, et al.
Publicado: (2013)

Estimating bonobo (Pan paniscus) and chimpanzee (Pan troglodytes) evolutionary history from nucleotide site patterns
por: Brand, Colin M., et al.
Publicado: (2022)

The complex evolutionary history of aminoacyl-tRNA synthetases
por: Chaliotis, Anargyros, et al.
Publicado: (2017)

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives
por: Zaneveld, Jesse R., et al.
Publicado: (2010)

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments
por: Seemann, Stefan E., et al.
Publicado: (2008)

Sequence comparison by sequence harmony identifies subtype-specific functional sites
por: Pirovano, Walter, et al.
Publicado: (2006)

Pattern preferences of DNA nucleotide motifs by polyamines putrescine(2+), spermidine(3+) and spermine(4+)
por: Perepelytsya, Sergiy, et al.
Publicado: (2019)

Identifying foldable regions in protein sequence from the hydrophobic signal
por: Pang, Chi N.I., et al.
Publicado: (2008)

Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets
por: Zhao, Huiying, et al.
Publicado: (2011)

Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences
por: Siebert, Matthias, et al.
Publicado: (2016)

Predicting translational diffusion of evolutionary conserved RNA structures by the nucleotide number
por: Werner, Arne
Publicado: (2011)

A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications
por: Pietrosanto, Marco, et al.
Publicado: (2016)

Sequence composition similarities with the 7SL RNA are highly predictive of functional genomic features
por: Paquet, Yanick, et al.
Publicado: (2010)

Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies
por: Salari, Raheleh, et al.
Publicado: (2013)

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction
por: Harmanci, Arif Ozgun, et al.
Publicado: (2008)

Improving the accuracy of predicting secondary structure for aligned RNA sequences
por: Hamada, Michiaki, et al.
Publicado: (2011)

Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions
por: Sükösd, Zsuzsanna, et al.
Publicado: (2013)

Pattern mining with evolutionary algorithms
por: Ventura, Sebastián, et al.
Publicado: (2016)

Molecular evolutionary and structural analysis of the cytosolic DNA sensor cGAS and STING
por: Wu, Xiaomei, et al.
Publicado: (2014)

Limits in accuracy and a strategy of RNA structure prediction using experimental information
por: Wang, Jian, et al.
Publicado: (2019)

Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs
por: Roux, Julien, et al.
Publicado: (2012)

TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs
por: Tan, Zhen, et al.
Publicado: (2017)

The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification
por: Majorek, Karolina A., et al.
Publicado: (2014)

Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq
por: Massarat, Arya R, et al.
Publicado: (2021)

A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs
por: Poblete, Simón, et al.
Publicado: (2018)

Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data
por: Wu, Yang, et al.
Publicado: (2015)

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction
por: Washietl, Stefan, et al.
Publicado: (2012)

RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information
por: Suresh, V., et al.
Publicado: (2015)

iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition
por: Lin, Hao, et al.
Publicado: (2014)

The evolutionary history of Stomatopoda (Crustacea: Malacostraca) inferred from molecular data
por: Van Der Wal, Cara, et al.
Publicado: (2017)

Bayesian prediction of RNA translation from ribosome profiling
por: Malone, Brandon, et al.
Publicado: (2017)

Computational learning on specificity-determining residue-nucleotide interactions
por: Wong, Ka-Chun, et al.
Publicado: (2015)

Topological constraints of RNA pseudoknotted and loop-kissing motifs: applications to three-dimensional structure prediction
por: Xu, Xiaojun, et al.
Publicado: (2020)

Evolutionary history of the TBP-domain superfamily
por: Brindefalk, Björn, et al.
Publicado: (2013)

Evolutionary determinants of genome-wide nucleotide composition
por: Long, Hongan, et al.
Publicado: (2018)

Cannot write session to /tmp/vufind_sessions/sess_unff1m1g4lnpfo8ps53i375ihs