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OSfinder: A Tool for Accurate Orthology Mapping

News

  • Public release of OSfinder v1.0 (Oct.02,2008)
  • Description

    The term orthologous segment(s) is defined as genomic segments in different organisms descended from common evolutionary ancestor without rearrangements. The problem of identifying orthologous segments is referred to as orthology mapping. OSfinder performs orthology mapping accurately by using Markov chain models and machine learning techniques.

    Input and Output

    OSfinder takes the coordinate spans for anchors as input, and reports the coordinate spans for chains and orthologous segments as output.


    Anchor -- A short homologous region detected among a set of genomes under comparison. Homologous genes or bidirectional local sequence matches are well used as anchors.

    Chain -- A genomic segment, in which anchors are densely and off-diagonally located.

    Orthologous Segment -- A genomic segment descended from common evolutionary ancestor without rearrangements.

    Dot-plot View

    Dot-plots provide us with a intuitive explanation for anchors, chains and orthologous segments. Here we show the dot-plots of anchors, chains and orthologous segments detected between human and mouse X chromosomes.
    anchor.jpg
    ======= Status of dot-plot =======
    " 8,243 anchors were plotted.
    " Ave. length was 104 bp.
    ==================================
    chain.jpg
    ======= Status of dot-plot =======
    " 419 chains were plotted.
    " Ave. length was 143,633 bp.
    ==================================
    os.jpg
    ======= Status of dot-plot =======
    " 10 segments were plotted.
    " Ave. length was 13,951,853 bp.
    ==================================