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Augustus is a program that predicts genes in eukaryotic genomic sequences. It can be run on this web server, on a new web server for larger input files or be downloaded and run locally. It has various features such as RNA-Seq integration, protein profile extension, automatic annotation pipeline, alternative splicing prediction and more.
- Mario Stanke
- 2003
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
- Gene Prediction with AUGUSTUS
- INTRODUCTION
- Windows
- Ubuntu 18.04, Debian 9 or later
- Docker
- Singularity
- Building AUGUSTUS from source
- WEB-SERVER
- REFERENCES AND DOCUMENTATION
- LICENSES
AUGUSTUS is a program to find genes and their structures in one or more genomes. More ...
Windows users can use the Windows Subsystem for Linux (WSL) to install AUGUSTUS exactly as described below for Linux. How to set up the WSL for AUGUSTUS is described here.
Until Ubuntu 21.04 and Debian 11 only as single-genome version, since then with capability for comparative gene prediction.
Create a docker image from Dockerfile using:
Create a Singularity Image File from the Singularity Definition File using
Install locally
As a normal user, add the directory of the executables to the PATH environment variable, for example:
Install globally
You can install AUGUSTUS globally, if you have root privileges, for example: Alternatively, you can exectue similar commands to those in the "install" section of the top-level Makefile to customize the global installation.
Optional: set environment variable AUGUSTUS_CONFIG_PATH
If the environment variable AUGUSTUS_CONFIG_PATH is set, augustus and etraining will look there for the config directory that contains the configuration and parameter files, e.g. '~/augustus/config'. You may want to add this line to a startup script (like ~/.bashrc). If this environment variable is not set, then the programs will look in the path ../config relative to the directory in which the executable lies. As a third alternative, you can specify this directory on the command line when you run augustus: --AUGUSTUS_CONFIG_PATH=/my_path_to_AUGUSTUS/augustus/config/
AUGUSTUS can also be run through a web-interface at http://bioinf.uni-greifswald.de/augustus/ and a web service at http://bioinf.uni-greifswald.de/webaugustus/.
Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics, 24(5), pages 637–644, doi: 10.1093/bioinformatics/btn013
For further references see docs/REFERENCES.md
All source code, i.e.
•the AUGUSTUS source code (src/*.cc, include/*.hh)
•the scripts (scripts/*)
•the auxiliary programs (auxprogs/)
•the tree-parser (src/scanner, src/parser)
•the unit tests (src/unittests)
Learn how to use AUGUSTUS, a software tool for ab initio and evidence-based gene prediction, with examples and parameters. See the output in GFF format and the protein sequences for the predicted genes.
Learn how to use Augustus, a gene prediction program that can incorporate extrinsic sources of gene structure, on Biowulf cluster. See documentation, example files, and interactive and batch job submission options.
AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic ...
Learn how to train AUGUSTUS for another species using genomic sequences with annotated gene structures. Follow the steps to create a meta parameters file, make an initial training, and test the accuracy of your model.
