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RepeatMasker is a tool to detect repeats and low complexity DNA sequences. The RepeatMasker can use nhmmer, cross_match, ABBlast, WUBlast, RMBlast, and Decypher for repeat detection, as well as Dfam and Repbase libraries. The RepeatMasker algorithm outputs annotation and a FASTA file with repeats masked, i.e., replaced by Ns by default.


Sequence analysis; Sequence composition, complexity and repeats



Tarailo-Graovac M, Chen N "Using RepeatMasker to identify repetitive elements in genomic sequences." Curr Protoc Bioinformatics, 2009
PMID: 19274634

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