AUGUSTUS: a web server for gene finding in eukaryotes

By Mario Stanke, Rasmus Steinkamp, Stephan Waack, Burkhard Morgenstern. Nucleic Acids Res., 2004

1,315 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/98cace1e39b6a6f63cc108ad20961b5328a49fea

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Genome Annotation in Plants and Fungi: EuGene as a Model Platform (2008, methodology): “The simple ab initio variant of EuGène is in agreement with AUGUSTUS, the best ab initio gene finder.”
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources (2006, background): “These user constraints can also be set at the AUGUSTUS web server [20].”
Genomics of the fungal kingdom: Insights into eukaryotic biology (2005, methodology): “These include GeneID (Guigo et al. 1992; Parra et al. 2000), FGenesh and FGenesh+ (Salamov and Solovyev 2000), SNAP (Korf 2004), Augustus (Stanke and Waack 2003; Stanke et al. 2004; Stanke and Morgenstern 2005), and GlimmerM (Salzberg et al. 1999).”
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database (2020, positive): “Onaparallel avenue, yet another algorithm, AUGUS-TUS (9–14), was demonstrated to be one of the most accurate gene prediction tools (15–17).”
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints (2005, methodology): “To make our tool available to the research community, we have set up a WWW server at GOBICS (Go¨ttingen Bioinformatics Compute Server) (9).”
Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life (2016, methodology): “5 (Stanke et al., 2004) with hidden Markov models generated using the Coprinopsis cinerea (Schaeff.”
TSEBRA: transcript selector for BRAKER (2021, methodology): “BRAKER1 uses GeneMark-ET [10–12] together with AUGUSTUS [13–17] and relies on RNA-seq data to support gene finder training and accurate prediction of gene structures.”
The UCSC Genome Browser Database: update 2006 (2005, background): “Other recent additions of contributed gene annotations or predictions in the human Genome Browser include Vega Genes, Vega Pseudogenes, ECgene (29), Twinscan (30), SGP (31), Geneid (32), Augustus (33), Yale Pseudogenes (34) and Superfamily (35).”