AUGUSTUS: ab initio prediction of alternative transcripts

By Mario Stanke, Oliver Keller, Irfan Gunduz, A. Hayes, Stephan Waack, Burkhard Morgenstern. Nucleic Acids Res., 2006

2,513 citations recorded by the source corpus.

AUGUSTUS is a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model, a probabilistic model of a sequence and its gene structure. Like most existing gene finders, the first version of AUGUSTUS returned one transcript per predicted gene and ignored the phenomenon of alternative splicing. Herein, we present a WWW server for an extended version of AUGUSTUS that is able to predict multiple splice variants. To our knowledge, this is the first ab initio gene finder that can predict multiple transcripts. In addition, we offer a motif searching facility, where user-defined regular expressions can be searched against putative proteins encoded by the predicted genes. The AUGUSTUS web interface and the downloadable open-source stand-alone program are freely available from .

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e711b5dc883b6f79b6a00d5b034bb427e989e987

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Citations in the corpus

The genome of the pear (Pyrus bretschneideri Rehd.) (2013, methodology): “Augustus (Stanke et al. 2006) and GlimmerHMM (Majoros et al. 2004) were used to perform de novo prediction based on the repeat-masked genome.”
Using native and syntenically mapped cDNA alignments to improve de novo gene finding (2008, background): “The gene predictions for human can be browsed and downloaded at the UCSC Genome Browser (http:// genome.ucsc.edu) Contact: mstanke@gwdg.de Supplementary information: Supplementary data are available at Bioinformatics online.”
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools (2011, methodology): “These spliced read alignments plus peptide data obtained for the TAIR9 release were used as an input for the Augustus gene prediction package (38) and the resulting gene models were categorized and manually reviewed (see Supplementary Figure S1).”
Predicting Genes in Single Genomes with AUGUSTUS (2018, background): “AUGUSTUS (Hoff & Stanke, 2013; König, Romoth, Gerischer, & Stanke, 2016; Stanke, Diekhans, Baertsch, & Haussler, 2008; Stanke et al., 2006a; Stanke, Schöffmann, Dahms, Morgenstern, & Waack, 2006b; Stanke, Steinkamp, Waack, & Morgenstern, 2004) is a tool for finding protein-coding genes and their…”
Opportunities and challenges Genome-wide analyses of alternative splicing in plants: (2008, positive): “Recently, this algorithm has been extended to predict multiple gene structures for each gene, some of which may represent biologically relevant alternative transcripts (Stanke et al. 2006a).”
A survey of best practices for RNA-seq data analysis (2016, neutral): “Gene-finding tools such as Augustus [28] can incorporate RNA-seq data to better annotate protein-coding transcripts, but perform worse on non-coding transcripts [29].”
Identification of protein coding regions in RNA transcripts (2014, methodology): “melanogaster transcripts generated in (3) by Cufflinks (18), Augustus (19), Velvet (20), Oases (21) and Exonerate (22) from co-ordinates of the exons of assembled transcripts as provided by the authors of (3).”
BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA (2023, neutral): “Traditional ab initio gene prediction methods rely on computational predictions by statistical models using genome sequence data alone, for example AUGUSTUS (Stanke et al., 2006) and GeneMark-ES (Lomsadze et al., 2005).”
Function of alternative splicing. (2005, neutral): “(Stanke et al., 2006b) 20 O. Kelemen et al. / Gene 514 (2013) 1–30”