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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
Augustus [job submission] Paste your sequence(s) here help....
- References
BMC Bioinformatics 7, 62. Mario Stanke and Burkhard...
- Predictions
Augustus [predictions] Predictions for Chlamydomonas...
- Datasets
comparative Augustus Drosophila clade: Files for the...
- Downloads
Download AUGUSTUS, tutorial and some species' parameters....
- Accuracy
AUGUSTUS is used in many genome annotation projects. Below...
- WebAUGUSTUS
AUGUSTUS is a program that predicts genes in eukaryotic...
- 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
People also ask
What is Augustus?
What is Augustus gene prediction?
Can Augustus predict multiple transcripts?
What is Augus program?
- 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)
Jul 1, 2005 · To make our tool available to the research community, we have set up a WWW server at GOBICS (Göttingen Bioinformatics Compute Server) . AUGUSTUS may be forced to predict an exon, an intron, a splice site, a translation start or a translation end point at a certain position in the sequence.
Nov 22, 2018 · The Bioinformatics section of the Current Protocols journal covers experimental design, methods, and analyses in bioinformatics. Abstract AUGUSTUS is a tool for finding protein-coding genes and their exon-intron structure in genomic sequences.
Jul 1, 2006 · Like most existing gene finders, the first version of AUGUSTUS returned one transcript per predicted gene and ignored the phenomenon of alternative splicing. Herein, we present a WWW server for an extended version of AUGUSTUS that is able to predict multiple splice variants.
