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  • DFam database: what on earth is a "cut and paste" repeat?

    Hi All,

    Downloaded some repeat-masking data from DFam (http://www.dfam.org/) and along with LINE, SINE, LTR etc repeats it includes a class called 'Cut and Paste' repeats. I have never heard of these and can't seem to find any reference to them in the literature or description of them on the website. Anyone know if there's some other common name for them, or does anyone know anything at all about them?

    Any help or pointers towards resources would be really appreciated

  • #2
    They must be direct repeats created by transposition of class II transposons: http://users.rcn.com/jkimball.ma.ult...ansposons.html

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    • #3
      Originally posted by GenoMax View Post
      They must be direct repeats created by transposition of class II transposons: http://users.rcn.com/jkimball.ma.ult...ansposons.html
      Thank you SO much - it seems this was a case of one of those things that is hard to google if you don't know what you're looking for. All the results I got from searching for "cut and paste" just picked it up as a turn of phrase in a ton of irrelevant papers. Now that your link has allowed me to search for type II transposons I found plenty of results.
      For the benefit of anyone else reading the thread, I found this paper very informative if you would like to check it out:

      Muñoz-López, Martín, and José L. García-Pérez. “DNA Transposons: Nature and Applications in Genomics.” Current Genomics 11.2 (2010): 115–128. PMC. Web. 8 Sept. 2015.http://www.ncbi.nlm.nih.gov/pmc/arti.../CG-11-115.pdf

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