title: Using RepeatMasker to identify repetitive elements in genomic sequences.
abstract: RepeatMasker is a popular software tool widely used in computational genomics to identify, classify, and mask repetitive elements, including low-complexity sequences and interspersed repeats. RepeatMasker searches for repetitive sequence by aligning the input genome sequence against a library of known repeats, such as Repbase. Here, we describe two Basic Protocols that provide detailed guidelines on how to use RepeatMasker, either via the Web interface or command-line Unix/Linux system, to analyze repetitive elements in genomic sequences. Sequence comparisons in RepeatMasker are usually performed by the alignment program cross_match, which requires significant processing time for larger sequences. An Alternate Protocol describes how to reduce the processing time using an alternative alignment program, such as WU-BLAST. Further, the advantages, limitations, and known bugs of the software are discussed. Finally, guidelines for understanding the results are provided.
authors.affiliation: Simon Fraser University, Burnaby, British Columbia, Canada.
authors.forename: Maja
authors.initials: M
authors.lastname: Tarailo-Graovac
authors.affiliation: Simon Fraser University, Burnaby, British Columbia, Canada.
authors.forename: Nansheng
authors.initials: N
authors.lastname: Chen
mesh_terms: D023281:Genomics / Q000379:methods*; D020407:Internet; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D014584:User-Computer Interface