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  • id0
    Senior Member
    • Sep 2012
    • 130

    RepeatMasker species

    RepeatMasker asks for the species as one of the arguments:
    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
    I can't seem to locate the RepeatMasker repeat database. Where can I find that?

    I tried using the web interface for RepeatMasker. That gives you species suggestions based on your input. It did not recognize my species. What is the proper thing to do in that situation? Is it okay to not specify species?

    What is the downside of not specifying species?

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