TSDfinder is a program that defines the boundaries of a retrotransposed element based on the presence of TSDs (target site duplications). The TSDfinder program consists of several steps, including merging and determining the boundaries of a retrotransposed element, obtaining sequences surrounding the retrotransposed element, detecting potential TSDs, and scoring TSDs.
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Szak ST, Pickeral OK, Makalowski W, Boguski MS, Landsman D, Boeke JD.
Molecular archeology of L1 insertions in the human genome
Genome Biol. 2002; 3(10): research0052.1–research0052.18.