The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
De novo identification of repeat families in large genomes
Abstract
MOTIVATION: De novo repeat family identification is a challenging algorithmic problem of great practical importance. As the number of genome sequencing projects increases, there is a pressing need to identify the repeat families present in large, newly sequenced genomes. We develop a new method for de novo identification of repeat families via extension of consensus seeds; our method enables a rigorous definition of repeat boundaries, a key issue in repeat analysis. RESULTS: Our RepeatScout algorithm is more sensitive and is orders of magnitude faster than RECON, the dominant tool for de novo repeat family identification in newly sequenced genomes. Using RepeatScout, we estimate that approximately 2% of the human genome and 4% of mouse and rat genomes consist of previously unannotated repetitive sequence. AVAILABILITY: Source code is available for download at http://www-cse.ucsd.edu/groups/bioinformatics/software.html
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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
Tandem 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
Mobile Elements: Drivers of Genome Evolution
Kazazian, H. H. (2004) · Science · doi:10.1126/science.1089670 · Cited by 1,922
Cited by
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1883 · Cited by 21,039
O'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1189 · Cited by 6,357
“Additional data types, including PhyloCSF (20), CpGIslands, RepeatMasker (21) and Cap analysis of gene expression (CAGE) data (22), are sometimes used as additional support.”
MethodRepeatModeler2 for automated genomic discovery of transposable element families
Flynn, J. M., Hubley, R., Goubert, C., Rosen, J., Clark, A. G., Feschotte, C., & Smit, A. F. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1921046117 · Cited by 3,848
Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences
Tarailo‐Graovac, M., & Chen, N. (2009) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0410s25 · Cited by 3,398
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
Metadata
- Authors
- Price, A. L., Jones, N. C., & Pevzner, P. A.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-06-01
- Volume
- 21
- Issue
- Suppl 1
- Pages
- i351-i358
- ISSN
- 0266-7061 (ISSN-L)
- 1367-4803
- 1460-2059
- OpenAlex
- W2144268209
- Cited by
- 2,152
- References
- 3
- FWCI
- 19.50
- Type
- journal article
- Language
- en
- Open access
- closed
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