Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences

The RepeatMasker program is used for identifying repetitive elements in nucleotide sequences for further detailed analyses. Users can run RepeatMasker remotely via a Web site, or, for larger input sequences, the program and its dependent programs may be downloaded and run locally on Unix/Linux computers. The protocols in this chapter detail how to use RepeatMasker both remotely and locally to extract repetitive elements data and mask these repetitive elements in nucleotide sequences.