Augustus Genes Track Settings
 
Augustus Gene Predictions   (All Genes and Gene Predictions tracks)

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Color track by codons: Help on codon coloring

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Data schema/format description and download
Assembly: D. melanogaster Apr. 2004 (BDGP R4/dm2)
Data last updated at UCSC: 2005-06-02

Description

This track shows predictions of the AUGUSTUS program, which predicts the coding parts of protein-coding genes. This program, which was written by Mario Stanke at the Department of Bioinformatics, University of Göttingen, Germany, is available through the GOBICS web server.

Display Conventions and Configuration

This track follows the display conventions for gene prediction tracks.

This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. Click the Help on codon coloring link for more information about this feature.

Methods

Augustus uses a generalized hidden Markov model (GHMM) that models coding and non-coding sequence, splice sites, the branch point region, translation start and end, and lengths of exons and introns. This version has been trained on a set of 400 Drosophila genes. These ab initio predictions were made using only the Drosophila genomic sequence; no homology information or transcribed sequences were used.

Credits

Thanks to Mario Stanke for providing these data.

References

Stanke, M. Gene prediction with a hidden Markov model. Ph.D. thesis, Universität Göttingen, Germany (2004).

Stanke M, Steinkamp R, Waack S, Morgenstern B. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W309-12. PMID: 15215400; PMC: PMC441517

Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25. PMID: 14534192