|RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. Sequence comparisons in RepeatMasker are performed by the program cross_match, an efficient implementation of the Smith-Waterman-Gotoh algorithm developed by Phil Green.|
|For further information see RepeatMasker Help|
You may use it to mask the sequence before using some programs. That allows you to eliminate non significant sequence portion, and the used programs will go faster and results will be shorter
Be caution : In some program N will be deleted, so the position numbers of the sequence will change.