Is Target Site Duplication Part Of Repeatmasker Annotation?

Question

[Biomonika (Noolean)]

Greetings to all,

I would like to ask if target site duplication sequences are part of RepeatMasker annotation? (output of the program)

Thanks a lot.

Answer 1

[SES]

RepeatMasker will just find regions of homology to a library of repeats using a specified search engine (e.g., wublast). It will report the percent composition and number of bases for each superfamily in a human-readable table, it will provide the coordinates of the matches in a separate file, and it will output a masked fasta file that will be created based on the input and the library of repeats used for masking. If you want fine-grained annotations like target site duplications, I suggest you try another program (depending on what you are interested in finding), or try to find a GFF file of annotations for your species.