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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 is open source so you can compile it for your computing platform. You can now run AUGUSTUS on the German MediGRID. This enables you to submit larger sequence ...
- Job Submission
web interface for Augustus, the gene prediction tool....
- References
AUGUSTUS: a web server for gene finding in eukaryotes...
- Predictions
Augustus [predictions] Predictions for Chlamydomonas...
- Job Submission
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)
Predicting Genes with AUGUSTUS. This tutorial describes various typical settings for predicting genes with AUGUSTUS. 1. PREDICT GENES AB INITIO. Ab initio prediction means that no other input is used than the target genome itself. Below, you will find examples of predictions that use evidence (hints), here we use none.
The output file <span class="result"><tt>augustus.abinitio.gff</tt></span> now contains the predicted gene structures in GFF format with additional comments (lines starting with #). <pre class="code"> # This output was generated with AUGUSTUS (version 2.5). ... # start gene g1 chr2R AUGUSTUS gene 7007533 7010935 0.02 - . g1 chr2R AUGUSTUS trans...
Jul 1, 2006 · AUGUSTUS is a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model, a probabilistic model of a sequence and its gene structure. Like most existing gene finders, the first version of AUGUSTUS returned one transcript per predicted gene and ignored the phenomenon of alternative splicing.
May 21, 2013 · AUGUSTUS is one of the most accurate tools for eukaryotic gene prediction. Here, we present WebAUGUSTUS, a web interface for training AUGUSTUS and predicting genes with AUGUSTUS. Depending on the needs of the user, WebAUGUSTUS generates training gene structures automatically.
