Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences
Top Cited Papers
Open Access
- 1 March 2009
- journal article
- unit
- Published by Wiley in Current Protocols in Bioinformatics
- Vol. 25 (1), 4.10.1-4.10.14
- https://doi.org/10.1002/0471250953.bi0410s25
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. Curr. Protoc. Bioinform. 25:4.10.1‐4.10.14. © 2009 by John Wiley & Sons, Inc.Keywords
This publication has 7 references indexed in Scilit:
- Repbase Update, a database of eukaryotic repetitive elementsCytogenetic and Genome Research, 2005
- De novo identification of repeat families in large genomesBioinformatics, 2005
- The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative GenomicsPLoS Biology, 2003
- Automated De Novo Identification of Repeat Sequence Families in Sequenced GenomesGenome Research, 2002
- MaskerAid : a performance enhancement to RepeatMaskerBioinformatics, 2000
- Repbase Update: a database and an electronic journal of repetitive elementsTrends in Genetics, 2000
- Identification of common molecular subsequencesJournal of Molecular Biology, 1981