An Improved Algorithm for Demarcating Bacterial Species

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For scientists to understand microbial ecosystems, identifying the fundamental unit of bacterial species is imperative. Past attempts involved characterizing metabolic capabilities, or percentage of genome sequence similarity; however these approaches have proven ineffective. The Cohan lab developed a program called Ecotype Simulation (ES) that attempts to demarcate bacterial species based on the Stable Ecotype model of speciation. Previously, our lab has demonstrated the superior accuracy of ES, compared to other demarcators (AdaptML, BAPS, GMYC), with field experiments and sequence simulations. However, ES lacks the efficiency of the other programs. Recently we have made several improvements to the algorithm behind ES that increase its efficiency by orders of magnitude. With these improvements I aim to demonstrate the high accuracy of our second version of Ecotype Simulation (ES2) compared to ES for smaller inputs and then show ES2's superiority for larger size inputs.

    Item Description
    Name(s)
    Thesis advisor: Krizanc, Danny
    Date
    May 23, 2013
    Extent
    68 pages
    Language
    eng
    Genre
    Physical Form
    electronic
    Discipline
    Rights and Use
    In Copyright – Non-Commercial Use Permitted
    Digital Collection
    PID
    ir:661