The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes
Open accessAbstract
Repetitive sequences make up a major part of eukaryotic genomes. We have developed an approach for the de novo identification and classification of repeat sequence families that is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. When tested on the human genome, our approach was able to properly identify and group known transposable elements. The program,RECON, should be useful for first-pass automatic classification of repeats in newly sequenced genomes. [The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: R. Klein.]
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DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
Morgenstern, B. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.3.211 · Cited by 678
Cited by
Assembly of long, error-prone reads using repeat graphs
Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0072-8 · Cited by 5,986
RepeatModeler2 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
Conservation and divergence of methylation patterning in plants and animals
Feng, S., Cokus, S. J., Zhang, X., Chen, P.-Y., Bostick, M., Goll, M. G., Hetzel, J., Jain, J., Strauss, S. H., Halpern, M. E., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002720107 · Cited by 1,285
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
Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears
Liu, S., Lorenzen, E. D., Fumagalli, M., Li, B., Harris, K., Xiong, Z., Zhou, L., Korneliussen, T. S., Somel, M., Babbitt, C., et al. (2014) · Cell · doi:10.1016/j.cell.2014.03.054 · Cited by 411
Metadata
- Authors
- Bao, Z., & Eddy, S. R.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2002-07-19
- Volume
- 12
- Issue
- 8
- Pages
- 1269-1276
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W2151899848
- Cited by
- 983
- References
- 1
- Type
- posted content
- Language
- en
- Open access
- bronze
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