UNIT 4.10 Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences
Published Online: 1 MAR 2009
Copyright © 2009 by John Wiley & Sons, Inc.
Lab Protocol Title
Current Protocols in Bioinformatics
How to Cite
Tarailo-Graovac, M. and Chen, N. 2009. Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences. Current Protocols in Bioinformatics. 25:4.10:4.10.1–4.10.14.
- Published Online: 1 MAR 2009
- Published Print: MAR 2009
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.
- genome annotation;
- repetitive elements;
- repeat library;