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  • Nucleic acid structure, Computational Methods  (2)
  • Computational Methods  (1)
  • Oxford University Press  (3)
  • American Geophysical Union (AGU)
  • Blackwell Publishing Ltd
  • Nature Publishing Group
  • 2010-2014  (3)
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  • Oxford University Press  (3)
  • American Geophysical Union (AGU)
  • Blackwell Publishing Ltd
  • Nature Publishing Group
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  • 2010-2014  (3)
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  • 1
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    Complete RNA inverse folding: computational design of functional hammerhead ribozymes (2014)
    Oxford University Press
    Details
    Publikationsdatum: 2014-10-10
    Beschreibung: Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st century. This paper concerns the synthetic design of ribonucleic acid molecules, using our recent algorithm, RNAiFold , which can determine all RNA sequences whose minimum free energy secondary structure is a user-specified target structure. Using RNAiFold , we design ten cis -cleaving hammerhead ribozymes, all of which are shown to be functional by a cleavage assay. We additionally use RNAiFold to design a functional cis -cleaving hammerhead as a modular unit of a synthetic larger RNA. Analysis of kinetics on this small set of hammerheads suggests that cleavage rate of computationally designed ribozymes may be correlated with positional entropy, ensemble defect, structural flexibility/rigidity and related measures. Artificial ribozymes have been designed in the past either manually or by SELEX (Systematic Evolution of Ligands by Exponential Enrichment); however, this appears to be the first purely computational design and experimental validation of novel functional ribozymes. RNAiFold is available at http://bioinformatics.bc.edu/clotelab/RNAiFold/ .
    Schlagwort(e): Computational Methods
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
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    R-CHIE: a web server and R package for visualizing RNA secondary structures (2012)
    Oxford University Press
    Details
    Publikationsdatum: 2012-06-28
    Beschreibung: Visually examining RNA structures can greatly aid in understanding their potential functional roles and in evaluating the performance of structure prediction algorithms. As many functional roles of RNA structures can already be studied given the secondary structure of the RNA, various methods have been devised for visualizing RNA secondary structures. Most of these methods depict a given RNA secondary structure as a planar graph consisting of base-paired stems interconnected by roundish loops. In this article, we present an alternative method of depicting RNA secondary structure as arc diagrams. This is well suited for structures that are difficult or impossible to represent as planar stem-loop diagrams. Arc diagrams can intuitively display pseudo-knotted structures, as well as transient and alternative structural features. In addition, they facilitate the comparison of known and predicted RNA secondary structures. An added benefit is that structure information can be displayed in conjunction with a corresponding multiple sequence alignments, thereby highlighting structure and primary sequence conservation and variation. We have implemented the visualization algorithm as a web server R- chie as well as a corresponding R package called R4RNA, which allows users to run the software locally and across a range of common operating systems.
    Schlagwort(e): Nucleic acid structure, Computational Methods
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
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    COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account (2013)
    Oxford University Press
    Details
    Publikationsdatum: 2013-05-04
    Beschreibung: Existing state-of-the-art methods that take a single RNA sequence and predict the corresponding RNA secondary structure are thermodynamic methods. These aim to predict the most stable RNA structure. There exists by now ample experimental and theoretical evidence that the process of structure formation matters and that sequences in vivo fold while they are being transcribed. None of the thermodynamic methods, however, consider the process of structure formation. Here, we present a conceptually new method for predicting RNA secondary structure, called C o F old , that takes effects of co-transcriptional folding explicitly into account. Our method significantly improves the state-of-art in terms of prediction accuracy, especially for long sequences of 〉1000 nt in length.
    Schlagwort(e): Nucleic acid structure, Computational Methods
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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