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AUGUSTUS specifications

Information


Unique identifier OMICS_07777
Name AUGUSTUS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


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Maintainers


  • person_outline Mario Stanke
  • person_outline Oliver Keller

Information


Unique identifier OMICS_07777
Name AUGUSTUS
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Mario Stanke
  • person_outline Oliver Keller

Publications for AUGUSTUS

AUGUSTUS citations

 (307)
library_books

Three previously unrecognised classes of biosynthetic enzymes revealed during the production of xenovulene A

2018
Nat Commun
PMCID: 5958101
PMID: 29773797
DOI: 10.1038/s41467-018-04364-9

[…] rching using the previously identified aspks1 gene rapidly identified a 1.6-Mb scaffold as containing a 49-kb BGC potentially involved in tropolone biosynthesis (Table ). Automatic gene prediction by Augustus 3.0 and annotation within the GenDBE platform revealed the presence of numerous genes with potential roles in secondary metabolism (Supplementary Fig. , Supplementary Table ). Previous work h […]

library_books

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

2018
MBio
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] t Finder v4.07b (), corresponding to fungal sequences from RepBase (). The genomes were annotated with the Funannotate v0.6.2 pipeline (https://github.com/nextgenusfs/funannotate), employing tools of Augustus (), GeneMark.hmm-ES (), and EVM (). Gene function was inferred from matches to the databases of Pfam (), Merops (), CAZy (), InterProScan (), and Swiss-Prot (). Product descriptions were assi […]

library_books

Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution

2018
BMC Genomics
PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] of repetitive elements with RepeatMasker v4.0.5 using the “Aves” repeat library [].We annotated scaffolds with a length of 1 kb or greater using MAKER v2.31.8 [] and conducted gene predictions using AUGUSTUS v3.2.1 [] with a hidden Markov model trained from Gallus gallus RefSeq sequences. In addition to ab initio gene prediction, we used homologous protein evidence for annotated genes from the am […]

library_books

Whole genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

2018
GigaScience
PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044

[…] RID:SCR_013048), version 2.0.6, [], was utilized to assemble transcripts, and PASA (version 2.0.0) [] was used to group alternatively spliced isoforms. For the ab initio gene prediction, the standard Augustus (version 3.0.3) pipeline was used to yield potentially predicted genes with evidence from both homologous proteins and RNA-seq. Next, the consensus gene set was determined by consolidating th […]

call_split

Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen fixing rhizobium symbioses

2018
Proc Natl Acad Sci U S A
PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115
call_split See protocol

[…] Finally, four gene-predictor tracks were used: (i) SNAP () trained on P. andersonii transdecoder transcript annotations; (ii) SNAP trained on T. orientalis transdecoder transcript annotations; (iii) Augustus (), as used in the BRAKER pipeline, trained on RNA-seq alignments (); and (iv) GeneMark-ET, as used in the BRAKER pipeline, trained on RNA-seq alignments ().First, all evidence tracks were pr […]

library_books

De Novo DNA Synthesis in Aedes aegypti Midgut Cells as a Complementary Strategy to Limit Dengue Viral Replication

2018
Front Microbiol
PMCID: 5932203
PMID: 29755433
DOI: 10.3389/fmicb.2018.00801

[…] blets in order to bind to its DNA elements (Ming et al., ). A map detailing the protein architecture is shown in Supplementary Figure .An exon prediction analysis was made using five different tools: Augustus (Keller et al., ), FGenesh (Salamov and Solovyev, ), GeneID (Blanco et al., ), GeneMark (Besemer and Borodovsky, ) and GenScan (Burge and Karlin, ). Hnt CDS and mRNA coding regions were deduc […]

Citations

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AUGUSTUS institution(s)
Institute of Computer Science, University of Gottingen, Gottingen, Germany; Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany; Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany
AUGUSTUS funding source(s)
Supported by the Deutsche Forschungsgemeinschaft (KO 2251/3-1, KO 2251/6-1 and WA 766/6-1).

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