The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
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. Curr. Protoc. Bioinform. 25:4.10.1‐4.10.14. © 2009 by John Wiley & Sons, Inc.
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Cites
Identification of common molecular subsequences
Smith, T. F., & Waterman, M. S. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90087-5 · Cited by 9,940
Repbase Update, a database of eukaryotic repetitive elements
Jurka, J., Kapitonov, V. V., Pavlicek, A., Klonowski, P., Kohany, O., & Walichiewicz, J. (2005) · Cytogenetic and Genome Research · doi:10.1159/000084979 · Cited by 3,370
De novo identification of repeat families in large genomes
Price, A. L., Jones, N. C., & Pevzner, P. A. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1018 · Cited by 2,152
Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes
Bao, Z., & Eddy, S. R. (2002) · Genome Research · doi:10.1101/gr.88502 · Cited by 983
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
Stein, L. D., Bao, Z., Blasiar, D., Blumenthal, T., Brent, M. R., Chen, N., Chinwalla, A., Clarke, L., Clee, C., Coghlan, A., et al. (2003) · PLoS Biology · doi:10.1371/journal.pbio.0000045 · Cited by 940
Self-citationRepbase Update: a database and an electronic journal of repetitive elements
Jurka, J. (2000) · Trends in Genetics · doi:10.1016/s0168-9525(00)02093-x · Cited by 883
MaskerAid : a performance enhancement to RepeatMasker
Bedell, J. A., Korf, I., & Gish, W. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.11.1040 · Cited by 282
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Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Gedman, G. L., et al. (2020) · doi:10.1101/2020.05.22.110833 · Cited by 3,097
Yang, J., Liu, D., Wang, X., Ji, C., Cheng, F., Liu, B., Hu, Z., Chen, S., Pental, D., Ju, Y., et al. (2016) · Nature Genetics · doi:10.1038/ng.3657 · Cited by 580
Vieler, A., Wu, G., Tsai, C.-H., Bullard, B., Cornish, A. J., Harvey, C., Reca, I.-B., Thornburg, C., Achawanantakun, R., Buehl, C. J., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1003064 · Cited by 458
Hughes, J. R., Roberts, N., McGowan, S., Hay, D., Giannoulatou, E., Lynch, M., De Gobbi, M., Taylor, S., Gibbons, R., & Higgs, D. R. (2014) · Nature Genetics · doi:10.1038/ng.2871 · Cited by 461
Metadata
- Authors
- Tarailo‐Graovac, M., & Chen, N.
- Venue
- Current Protocols in Bioinformatics
- Publisher
- Wiley
- Published
- 2009-03
- Volume
- 25
- Issue
- 1
- Pages
- 4.10.1-4.10.14
- ISSN
- 1934-3396 (ISSN-L)
- 1934-340X
- OpenAlex
- W2159038577
- Cited by
- 3,398
- References
- 7
- FWCI
- 26.83
- Type
- journal article
- Language
- en
- Open access
- closed
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