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AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. Augustus [gene prediction] University of Göttingen - Faculty of Biology - Institute of Microbiology and Genetics - Department of Bioinformatics
AUGUSTUS is used in many genome annotation projects. Below are some accuracy values in comparison to other programs. As accuracy measure we use sensitivity (Sn) and specificity (Sp).
851 single gene sequences predicted by genewise and compiled by Jason Stajich. 261 genes are complete, 590 genes are incomplete at the 3' end. Genes redundand with those in the Genbank annotations were deleted:
Which values for X are possible is specified in the file augustus/config/extrinsic.cfg, e.g. X=M, E, or P. AUGUSTUS can follow a hint, i.e. predict a gene structure that is compatible with it, or AUGUSTUS can ignore a hint, i.e. predict a gene structure that is not compatible with it.
Genome papers, where AUGUSTUS was used in collaboration: Tribolium Genome Sequencing Consortium, The genome of the model beetle and pest Tribolium castaneum. Nature , March 2008.
Augustus [predictions] Predictions for Chlamydomonas rheinhardtii. Predictions for 4 Caenorhabditis species: C.elegans (WS 180), C.brenneri (PB2801, assembly 1), C.briggsae (CB3), C.remanei (assembly 2) Predictions for the whole genome of Drosophila melagonaster (Release 4 assembly of the Drosophila melanogaster genome, dm2, Apr. 2004) Predictions for the whole genome of Homo sapiens
AUGUSTUS was trained in collaboration with Erik F.Y. Hom (Harvard) and Chun Liang (Miami University, Ohio) on Chlamydomonas reinhardtii. These predictions are based on the JGI-Assembly v4. We thank the Joint Genome Institute/Stanford Human Genome Center for giving us access to version 4 of the Chlamydomonas genome.
Among all gene structures that are consistent and that obey all user constraints, AUGUSTUS finds the most likely gene structure. A user constraints may contradict the biological consistency. For example a donor splice site where there is no GT in the sequence.
Introduction ----- The purpose of this pipeline script is to run the AUGUSTUS training process and gene prediction algorithm automatically on a given eukaryotic genome with available cDNA evidence. The complete process contains the following steps.
The general approach is to generate hints for Augustus from the RNA-Seq, which can be used together with hints from other sources if available (like from an existing gene models, ESTs, protein or genomic conservation, MS/MS).
