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  • Geomagnetism, Rock Magnetism and Palaeomagnetism  (1)
  • Nucleic acid structure, RNA characterisation and manipulation, Computational Methods  (1)
  • Oxford University Press  (2)
  • Molecular Diversity Preservation International (MDPI)
  • Blackwell Publishing Ltd
  • Nature Publishing Group
  • 1
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    A comprehensive comparison of general RNA-RNA interaction prediction methods (2016)
    Oxford University Press
    Details
    Publication Date: 2016-04-21
    Description: RNA–RNA interactions are fast emerging as a major functional component in many newly discovered non-coding RNAs. Basepairing is believed to be a major contributor to the stability of these intermolecular interactions, much like intramolecular basepairs formed in RNA secondary structure. As such, using algorithms similar to those for predicting RNA secondary structure, computational methods have been recently developed for the prediction of RNA–RNA interactions. We provide the first comprehensive comparison comprising 14 methods that predict general intermolecular basepairs. To evaluate these, we compile an extensive data set of 54 experimentally confirmed fungal snoRNA–rRNA interactions and 102 bacterial sRNA–mRNA interactions. We test the performance accuracy of all methods, evaluating the effects of tool settings, sequence length, and multiple sequence alignment usage and quality. Our results show that—unlike for RNA secondary structure prediction—the overall best performing tools are non-comparative energy-based tools utilizing accessibility information that predict short interactions on this data set. Furthermore, we find that maintaining high accuracy across biologically different data sets and increasing input lengths remains a huge challenge, causing implications for de novo transcriptome-wide searches. Finally, we make our interaction data set publicly available for future development and benchmarking efforts.
    Keywords: Nucleic acid structure, RNA characterisation and manipulation, 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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