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
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