The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
PILER: identification and classification of genomic repeats
Abstract
SUMMARY: Repeated elements such as satellites and transposons are ubiquitous in eukaryotic genomes. De novo computational identification and classification of such elements is a challenging problem. Therefore, repeat annotation of sequenced genomes has historically largely relied on sequence similarity to hand-curated libraries of known repeat families. We present a new approach to de novo repeat annotation that exploits characteristic patterns of local alignments induced by certain classes of repeats. We describe PILER, a package of efficient search algorithms for identifying such patterns. Novel repeats found using PILER are reported for Homo sapiens, Arabidopsis thalania and Drosophila melanogaster. AVAILABILITY: The PILER software is freely available at http://www.drive5.com/piler.
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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Self-citationMUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
Self-citationInitial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
Self-citationTandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Edgar, R. C. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-113 · Cited by 8,970
Self-citationThe evolutionary dynamics of repetitive DNA in eukaryotes
Charlesworth, B., Sniegowski, P., & Stephan, W. (1994) · Nature · doi:10.1038/371215a0 · Cited by 1,623
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
Repbase 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
Celniker, S. E., Wheeler, D. A., Kronmiller, B., Carlson, J. W., Halpern, A., Patel, S., Adams, M., Champe, M., Dugan, S. P., Frise, E., et al. (2002) · Genome Biology · doi:10.1186/gb-2002-3-12-research0079 · Cited by 387
Self-citation
Cited by
Evolution of genes and genomes on the Drosophila phylogeny
Drosophila 12 Genomes Consortium (2007) · Nature · doi:10.1038/nature06341 · Cited by 2,010
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
Ellinghaus, D., Kurtz, S., & Willhoeft, U. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-18 · Cited by 1,641
The genome of the cucumber,Cucumis sativus L
Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., Lucas, W. J., Wang, X., Xie, B., Ni, P., et al. (2009) · Nature Genetics · doi:10.1038/ng.475 · Cited by 1,490
Genome Sequence of the Pea Aphid Acyrthosiphon pisum
The International Aphid Genomics Consortium (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000313 · Cited by 1,314
Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
de Koning, A. P. J., Gu, W., Castoe, T. A., Batzer, M. A., & Pollock, D. D. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002384 · Cited by 1,112
Metadata
- Authors
- Edgar, R. C., & Myers, E. W.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-06-01
- Volume
- 21
- Issue
- Suppl 1
- Pages
- i152-i158
- ISSN
- 0266-7061 (ISSN-L)
- 1367-4803
- 1460-2059
- OpenAlex
- W2122954888
- Cited by
- 718
- References
- 13
- FWCI
- 18.36
- Type
- journal article
- Language
- en
- Open access
- closed
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