Description

This track shows predictions of AUGUSTUS. AUGUSTUS is available through the GOBICS web server.

Display Conventions and Configuration

This annotation follows the display conventions for composite tracks. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. This track also 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 1284 human genes.

Augustus Gene Predictions Using Hints

This subtrack was made using hints from several other tracks:

Human mRNAs and Spliced Human ESTs aligned with BLAT
TransMapped RefSeq genes from mouse, rat, zebrafish, chicken, cow, Xenopus tropicalis, dog and chimpanzee
Retroposed Genes
Exoniphy

Augustus De Novo Gene Predictions

This subtrack was made using only the target genome sequence and evolutionary conservation. The conservation information was extracted from the Exoniphy track. Further, hints about retroposed genes were used, that are based only on previous de novo predictions of AUGUSTUS. No transcribed sequences were used for this track.

Augustus Ab Initio Gene Predictions

These predictions were made using only the genomic sequence; no conservation, homology information or transcribed sequence was used.

Credits

The Augustus subtracks were created by Mario Stanke. The TransMap track was created by Mark Diekhans, the Retroposed Genes tracks by Robert Baertsch, and the Exoniphy track by Adam Siepel's group.

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. Nucl Acids Res. 2004 Jul 1;32(Web Server Issue):W309-12.

Stanke M, Tzvetkova A, Morgenstern B. AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome. Genome Biology. 2006;7(Suppl 1):S11.

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