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  • Nucleic acid structure, Computational Methods  (2)
  • Geomagnetism, Rock Magnetism and Palaeomagnetism  (1)
  • Oxford University Press  (3)
  • Deutsches GeoForschungsZentrum GFZ
  • Institute of Physics
  • National Academy of Sciences
  • 2010-2014  (3)
  • 2000-2004
  • 1920-1924
Collection
Keywords
Publisher
  • Oxford University Press  (3)
  • Deutsches GeoForschungsZentrum GFZ
  • Institute of Physics
  • National Academy of Sciences
Years
  • 2010-2014  (3)
  • 2000-2004
  • 1920-1924
Year
  • 1
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    R-CHIE: a web server and R package for visualizing RNA secondary structures (2012)
    Oxford University Press
    Details
    Publication Date: 2012-06-28
    Description: 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.
    Keywords: Nucleic acid structure, Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Calibration of SQUID vector magnetometers in full tensor gradiometry systems (2014)
    Oxford University Press
    Details
    Publication Date: 2014-06-28
    Description: Measurement of magnetic vector or tensor quantities, namely of field or field gradient, delivers more details of the underlying geological setting in geomagnetic prospection than a scalar measurement of a single component or of the scalar total magnetic intensity. Currently, highest measurement resolutions are achievable with superconducting quantum interference device (SQUID)-based systems. Due to technological limitations, it is necessary to suppress the parasitic magnetic field response from the SQUID gradiometer signals, which are a superposition of one tensor component and all three orthogonal magnetic field components. This in turn requires an accurate estimation of the local magnetic field. Such a measurement can itself be achieved via three additional orthogonal SQUID reference magnetometers. It is the calibration of such a SQUID reference vector magnetometer system that is the subject of this paper. A number of vector magnetometer calibration methods are described in the literature. We present two methods that we have implemented and compared, for their suitability of rapid data processing and integration into a full tensor magnetic gradiometry, SQUID-based, system. We conclude that the calibration routines must necessarily model fabrication misalignments, field offset and scale factors, and include comparison with a reference magnetic field. In order to enable fast processing on site, the software must be able to function as a stand-alone toolbox.
    Keywords: Geomagnetism, Rock Magnetism and Palaeomagnetism
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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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
    Publication Date: 2013-05-04
    Description: 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.
    Keywords: Nucleic acid structure, Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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