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Gene identification in novel eukaryotic genomes by self-training algorithm
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“The reason for masking repeats is that ab initio gene prediction programs such as AUGUSTUS (96) or GeneMark (97) need to be trained, i.e., optimized for the specific species with regards to codon bias and splicing signals, and this training can be biased by repeats.”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [97]
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Cites
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<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
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“two picks, the first and rather sharp one at 60 nt and the second one at 300 nt (43).”
Background
Research works printed but not linked: 37
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Cited by
Sorted by citations
Gabriel, L., Brůna, T., Hoff, K. J., Ebel, M., Lomsadze, A., Borodovsky, M., & Stanke, M. (2024) · Genome Research · doi:10.1101/gr.278090.123 · Cited by 676
Self-citationTørresen, O. K., Star, B., Mier, P., Andrade-Navarro, M. A., Bateman, A., Jarnot, P., Gruca, A., Grynberg, M., Kajava, A. V., Promponas, V. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz841 · Cited by 347
Pérez-Cobas, A. E., Gomez-Valero, L., & Buchrieser, C. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000409 · Cited by 314
The Capsaspora genome reveals a complex unicellular prehistory of animals
Suga, H., Chen, Z., de Mendoza, A., Sebé-Pedrós, A., Brown, M. W., Kramer, E., Carr, M., Kerner, P., Vervoort, M., Sánchez-Pons, N., et al. (2013) · Nature Communications · doi:10.1038/ncomms3325 · Cited by 317
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Metadata
- Authors
- Lomsadze, A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-11-27
- Volume
- 33
- Issue
- 20
- Pages
- 6494-6506
- ISSN
- 0305-1048
- 1362-4962
- PMC
- PMC1298918
- Cited by
- 975
- References
- 3
- Language
- en
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