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  • what's the default species when using repeatmasker

    I used the repeatmasker to predict the repeats, However the result is far lower than the reported, what's the problem?

    I have tested the result is different when you use choose different species for the species option? what's the default species in repeatmasker. In the old version, it default human.

  • #2
    Not sure what your desired genome is but UCSC has several masked genomes on their site. Maybe you can get a readymade file?

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    • #3
      Originally posted by genericforms View Post
      Not sure what your desired genome is but UCSC has several masked genomes on their site. Maybe you can get a readymade file?
      my desired genome is not presented in the RepBase. for I havenot multiple repeats of my genome, so I had to choose the species which is near to my genome in evolution.

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      • #4
        The default library (when no custom library is specified with the "-lib" option) is a database of repeat proteins in the "Libraries" directory of your RepeatMasker installation.

        There is also the "-species" option that will allow you to specify one library for masking.

        Code:
        -species <query species>
                Specify the species or clade of the input sequence. The species name
                must be a valid NCBI Taxonomy Database species name and be contained
                in the RepeatMasker repeat database. Some examples are:
        
                  -species human
                  -species mouse
                  -species rattus
                  -species "ciona savignyi"
                  -species arabidopsis
        
                Other commonly used species:
        
                mammal, carnivore, rodentia, rat, cow, pig, cat, dog, chicken, fugu,
                danio, "ciona intestinalis" drosophila, anopheles, elegans,
                diatoaea, artiodactyl, arabidopsis, rice, wheat, and maize

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        • #5
          you could try "-species all"

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