Browsing by Subject "algorithm"

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  • Truong Nguyen, Phuoc; Garcia-Valle, Santiago; Puigbo, Pere (2021)
    Early characterization of emerging viruses is essential to control their spread, such as the Zika Virus outbreak in 2014. Among other non-viral factors, host information is essential for the surveillance and control of virus spread. Flaviviruses (genus Flavivirus), akin to other viruses, are modulated by high mutation rates and selective forces to adapt their codon usage to that of their hosts. However, a major challenge is the identification of potential hosts for novel viruses. Usually, potential hosts of emerging zoonotic viruses are identified after several confirmed cases. This is inefficient for deterring future outbreaks. In this paper, we introduce an algorithm to identify the host range of a virus from its raw genome sequences. The proposed strategy relies on comparing codon usage frequencies across viruses and hosts, by means of a normalized Codon Adaptation Index (CAI). We have tested our algorithm on 94 flaviviruses and 16 potential hosts. This novel method is able to distinguish between arthropod and vertebrate hosts for several flaviviruses with high values of accuracy (virus group 91.9% and host type 86.1%) and specificity (virus group 94.9% and host type 79.6%), in comparison to empirical observations. Overall, this algorithm may be useful as a complementary tool to current phylogenetic methods in monitoring current and future viral outbreaks by understanding host-virus relationships.
  • Lehtola, Ville; Hyyti, Heikki; Keränen, Pekka; Kostamovaara, Juha (Copernicus Publications, 2019)
    The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences
    Single photon lidars (in solid state form) offer several benefits over pulsed lidars, such as independence of micro-mechanical moving parts or rotating joints, lower power consumption, faster acquisition rate, and reduced size. When mass produced, they will be cheaper and smaller and thus very attractive for mobile laser scanning applications. However, as these lidars operate by receiving single photons, they are very susceptible to background illumination such as sunlight. In other words, the observations contain a significant amount of noise, or to be specific, outliers. This causes trouble for measurements done in motion, as the sampling rate (i.e. the measurement frequency) should be low and high at the same time. It should be low enough so that target detection is robust, meaning that the targets can be distinguished from the single-photon avalanche diode (SPAD) triggings caused by the background photons. On the other hand, the sampling rate should be high enough to allow for measurements to be done from motion. Quick sampling reduces the probability that a sample gathered during motion would contain data from more than a single target at a specific range. Here, we study the exploitation of spatial correlations that exist between the observations as a mean to overcome this sampling rate paradox. We propose computational methods for short and long range. Our results indicate that the spatial correlations do indeed allow for faster and more robust sampling of measurements, which makes single photon lidars more attractive in (daylight) mobile laser scanning.
  • Holm, Liisa (Humana press, 2020)
    Methods in Molecular Biology
    The exponential growth in the number of newly solved protein structures makes correlating and classifying the data an important task. Distance matrix alignment (Dali) is used routinely by crystallographers worldwide to screen the database of known structures for similarity to newly determined structures. Dali is easily accessible through the web server (http://ekhidna.biocenter.helsinki.fi/dali). Alternatively, the program may be downloaded and pairwise comparisons performed locally on Linux computers. © 2020, Springer Science+Business Media, LLC, part of Springer Nature.