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MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
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MAKER2 does not train the ab initio models automatically.
“Although MAKER2 can provide training sets for SNAP and AUGUSTUS, it does not train the ab initio models automatically.”
From BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA (2024) · cites this paper as Holt and Yandell 2011
MAKER2 was designed to be used with a smaller protein database.
“Funannotate failed to run on most of the large OrthoDB-based protein databases, and MAKER2 was designed to be used with a smaller protein database, too.”
From BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA (2024) · cites this paper as Holt and Yandell 2011
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Cites
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
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
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-citationInitial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
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Research works printed but not linked: 53
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Metadata
- Authors
- Holt, C., & Yandell, M.
- Venue
- BMC Bioinformatics
- Published
- 2011-12
- Volume
- 12
- Issue
- 1
- ISSN
- 1471-2105
- PMC
- PMC3280279
- Cited by
- 2,118
- References
- 4
- Language
- en
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