AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
By Mario Stanke, Burkhard Morgenstern. Nucleic Acids Res., 2005
1,439 citations recorded by the source corpus.
We present a WWW server for AUGUSTUS, a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model, a probabilistic model of a sequence and its gene structure. The web server allows the user to impose constraints on the predicted gene structure. A constraint can specify the position of a splice site, a translation initiation site or a stop codon. Furthermore, it is possible to specify the position of known exons and intervals that are known to be exonic or intronic sequence. The number of constraints is arbitrary and constraints can be combined in order to pin down larger parts of the predicted gene structure. The result then is the most likely gene structure that complies with all given user constraints, if such a gene structure exists. The specification of constraints is useful when part of the gene structure is known, e.g. by expressed sequence tag or protein sequence alignments, or if the user wants to change the default prediction. The web interface and the downloadable stand-alone program are available free of charge at .
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/fd66b6c32b5e10425957d33e55082c603511bcb9
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In Molecular Biology
- Mario Stanke
- Mark Yandell
- Burkhard Morgenstern
- Carson Holt
- Mark Borodovsky
- Stephan Waack
- Alexandre Lomsadze
- Ian Korf
Citations in the corpus
- AUGUSTUS: ab initio prediction of alternative transcripts (2006, methodology): “Tomake AUGUSTUS available to the research community, we set up a WWW server at Go¨ttingen Bioinformatics Compute Server (GOBICS) (14,15).”
- MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. (2007, background): “Augustus is also trainable and comes with an optimization script that tries to find values for the metaparameters, such as splice window sizes (Stanke and Morgenstern 2005).”
- 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).”