analysis transposable elements repeatmasker

Question

[SeaStar]

hello, I'm analyzing my genome to find transposon. I make the first analysis with repeatmasker and here there are some elements that I found and their abundance. My question is: what does it mean the ? next to some elements? It is an error of repeatmasker or are elements recognized by repeatmasker that could be considered as....?

THis is the table:

table:

             DNA?  DNA/hAT-Ac   DNA/hAT-Charlie      DNA/hAT-Tag1    DNA/hAT-Tip100     
               5      84               276               2                71               
     DNA/PiggyBac DNA/TcMar-Mariner     DNA/TcMar-Tc1   LINE/CR1      LINE/Dong-R4 
          10               601                17         16               196               

         LTR/ERV1          LTR/ERVK          LTR/ERVL    LTR/Gypsy   LTR/Gypsy?                                                                          
           2                16               2                49        128 

            snRNA            srpRNA              tRNA           Unknown 
               39                 7               102                 1

[lieven.sterck]

Not directly related to your question but would it be possible to check the formatting of that table? Or is this an R-object or such (hence the 'R' tag on your question)

[SeaStar]

Yes it is an R object but I cannot explain the LTR/gypsy with and without ?

[lieven.sterck]

no expert but my guess would be 'known' and 'putative/potential' elements .

This also does not look like any of the ReepatMakser output files. How did you get this in that R-object? aka, what steps have you done between running RepeatMaker and printing this R object?

Answer 1

[AK]

The response from Robert Hubley (one of the developers of this tool) at SEQanswers in 2013:

The "?" following either a class for subclass is an indication that the curator is not confident in the call of the class or subclass. As we learn more about the element in question the classification is either changed or the "?" designation is removed.

[SeaStar]

Ok!! Thank you for the answer. So I'll considered them as the designed elements.