The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Predicting Genes in Single Genomes with AUGUSTUS
Abstract
AUGUSTUS is a tool for finding protein‐coding genes and their exon‐intron structure in genomic sequences. It does not necessarily require additional experimental input, as it can be applied in so‐called ab initio mode. However, extrinsic evidence from various sources such as transcriptome sequencing or the annotations of closely related genomes can be integrated in order to improve the accuracy and completeness of the annotation. AUGUSTUS can be applied to single genomes, or simultaneously to several aligned genomes. Here, we describe steps required for training AUGUSTUS for the annotation of individual genomes and the steps to do the actual structural annotation. Further, we describe the generation and integration of evidence from various sources of extrinsic evidence. © 2018 by John Wiley & Sons, Inc.
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“Augustus is an ab initio gene prediction tool, which uses a generalized hidden Markov model (HMM) for gene prediction.”
From Annotation matters: the effect of structural gene annotation on orthology inference (2025) · cites this paper as Hoff and Stanke 2019
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“Extrinsic evidence such as transcriptome sequences or annotations of closely related genomes can be provided as additional files, which modify the probabilities during prediction (Stanke and Waack 2003, Hoff and Stanke 2019).”
From Annotation matters: the effect of structural gene annotation on orthology inference (2025) · cites this paper as Hoff and Stanke 2019
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Cites
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<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
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Annotation matters: the effect of structural gene annotation on orthology inference
Prieto-Baños, S., Nevers, Y., Altenhoff, A., Warwick Vesztrocy, A., Dessimoz, C., & Glover, N. M. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf365 · Cited by 19
Advancing the Indian Cattle Pangenome: Characterizing Non-Reference Sequences in Bos indicus
Azam, S., Sahu, A., Pandey, N. K., Neupane, M., Van Tassell, C. P., Rosen, B. D., Gandham, R. K., Rath, S. N., & Majumdar, S. S. (2025) · Journal of Animal Science and Biotechnology · doi:10.1186/s40104-024-01133-1 · Cited by 5
Metadata
- Authors
- Hoff, K. J., & Stanke, M.
- Affiliations
- University of Greifswald, Institute of Mathematics and Computer Science Greifswald Germany
- Venue
- Current Protocols in Bioinformatics
- Publisher
- Wiley
- Published
- 2018-11-22
- Volume
- 65
- Issue
- 1
- ISSN
- 1934-3396
- 1934-340X
- Cited by
- 421
- References
- 2
- Language
- en
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