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    This study introduces CREx2, an algorithm for the weighted preserving Genome Sorting Problem (wpGSP). CREx2 efficiently finds the minimum weight sequence of genome rearrangement operations, particularly useful for fungal mitochondrial genome analysis.

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    Area of Science:

    • Computational Biology
    • Bioinformatics
    • Genomics

    Background:

    • The preserving Genome Sorting Problem (pGSP) involves finding the shortest sequence of operations to transform one gene order to another, preserving common intervals.
    • The weighted version (wpGSP) assigns costs to operations, seeking a minimum weight sequence.

    Purpose of the Study:

    • To present CREx2, an exact algorithm for solving the weighted preserving Genome Sorting Problem (wpGSP).
    • To evaluate the efficiency and applicability of CREx2 for phylogenetic analysis using real genomic data.

    Main Methods:

    • Developed the CREx2 algorithm to solve the wpGSP for arbitrary gene orders.
    • Incorporated rearrangement operations including inversions, transpositions, inverse transpositions, and tandem duplication random loss.
    • Analyzed algorithmic runtime, noting linear complexity for linearly structured common intervals.

    Main Results:

    • CREx2 provides an exact solution for the wpGSP.
    • The algorithm exhibits exponential worst-case runtime but linear runtime for specific interval structures.
    • Empirical testing on fungal mitochondrial genomes demonstrated CREx2's efficiency and utility.

    Conclusions:

    • CREx2 is an effective tool for solving the wpGSP.
    • The algorithm's performance is suitable for phylogenetic analyses, particularly with fungal mitochondrial genomes.