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. 2004 Jul 1;32(Web Server issue):W309-12.
doi: 10.1093/nar/gkh379.

AUGUSTUS: a web server for gene finding in eukaryotes

Mario Stanke  1 , Rasmus Steinkamp, Stephan Waack, Burkhard Morgenstern
Affiliations

AUGUSTUS: a web server for gene finding in eukaryotes

Mario Stanke et al. Nucleic Acids Res. .

Abstract

We present a www server for AUGUSTUS, a novel software program for ab initio gene prediction in eukaryotic genomic sequences. Our method is based on a generalized Hidden Markov Model with a new method for modeling the intron length distribution. This method allows approximation of the true intron length distribution more accurately than do existing programs. For genomic sequence data from human and Drosophila melanogaster, the accuracy of AUGUSTUS is superior to existing gene-finding approaches. The advantage of our program becomes apparent especially for larger input sequences containing more than one gene. The server is available at http://augustus.gobics.de.

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Figures

Figure 1
Figure 1
An example where the option ‘ignore conflicts with other strand’ helps. The lines in (a) show two nested Drosophila genes as annotated in FlyBase (12). The nine-exon gene on the forward strand includes a two-exon gene on the reverse strand within a long intron. The lines in (b) show the prediction with the default parameters. The gene on the forward strand is split into two genes by introducing two very short false positive exons so that the three predicted genes do not overlap. The lines in (c) show the prediction with the option ‘ignore conflicts with other strand’, which is identical to the annotation except for a short missed exon. This graphic has been obtained using gff2ps (13) from http://genome.imim.es/software/gfftools/GFF2PS.html.
See this image and copyright information in PMC

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