WindowMasker: window-based masker for sequenced genomes

@article{Morgulis2006WindowMaskerWM,
  title={WindowMasker: window-based masker for sequenced genomes},
  author={Aleksandr Morgulis and E. Michael Gertz and Alejandro A. Sch{\"a}ffer and Richa Agarwala},
  journal={Bioinformatics},
  year={2006},
  volume={22 2},
  pages={134-41}
}
MOTIVATION Matches to repetitive sequences are usually undesirable in the output of DNA database searches. Repetitive sequences need not be matched to a query, if they can be masked in the database. RepeatMasker/Maskeraid (RM), currently the most widely used software for DNA sequence masking, is slow and requires a library of repetitive template sequences… CONTINUE READING