UsingRepeatMasker超详细说明书.pdf

Using RepeatMasker to Identify UNIT 4.10 Repetitive Elements in Genomic Sequences Maja Tarailo-Graovac1 and Nansheng Chen1 1Simon Fraser University, Burnaby, British Columbia, Canada 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 C results are provided. Curr. Protoc. Bioinform. 25:4.10.1-4.10.14. 2009 by John Wiley Sons, Inc. Keywords: RepeatMasker genome annotation repetitive elements repeat library cross match WU-BLAST RECON INTRODUCTION RepeatMasker (developed by A.F.A. Smit, R. Hubley, and P. Green; see /) was designed to identify and annotate repetitive elements in nucleotide sequences and mask them for further analysis. The repetitive elements, including low-complexity DNA sequences and interspersed repeats, are annotated and replaced by Ns, Xs, or lowercase letters (see below for options) in the correspond- ing pos