what's the default species when using repeatmasker

[heiya]

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.

[adaptivegenome]

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

[heiya]

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.

[SES]

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.

-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

[059]

you could try "-species all"