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  1. bioinf.uni-greifswald.de › augustusAugustus: gene prediction - uni-greifswald

    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 ...

    • Predictions

      Augustus [predictions] Predictions for Chlamydomonas...

    • References

      AUGUSTUS at EGASP: using EST, protein and genomic alignments...

    • Downloads

      Augustus [downloads] Download AUGUSTUS, tutorial and some...

    • Job Submission

      Augustus [job submission] Paste your sequence(s) here help....

    • Datasets

      Augustus. The following sequence files were used to train...

    • Accuracy

      AUGUSTUS is used in many genome annotation projects. Below...

  2. augustus.gobics.deAugustus: gene prediction

    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

  3. github.com › Gaius-Augustus › AugustusGaius-Augustus/Augustus: Genome annotation with AUGUSTUS - GitHub

    • 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
    INTRODUCTION
    INSTALLATION
    RUNNING AUGUSTUS
    WEB-SERVER
    COMPARATIVE GENE PREDICTION
    AUTHORS AND CONTACT

    See full list on github.com

    AUGUSTUS is a program to find genes and their structures in one or more genomes. More ...

    See full list on github.com

    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.

    See full list on github.com

    Until Ubuntu 21.04 and Debian 11 only as single-genome version, since then with capability for comparative gene prediction.

    See full list on github.com

    Create a docker image from Dockerfile using:

    See full list on github.com

    Create a Singularity Image File from the Singularity Definition File using

    See full list on github.com

    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/

    See full list on github.com

    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/.

    See full list on github.com

    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

    See full list on github.com

    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)

    See full list on github.com

  4. bioinf.uni-greifswald.de › augustus › downloadsAugustus: downloads - uni-greifswald

    Augustus [downloads] Download AUGUSTUS, tutorial and some species' parameters. AUGUSTUS has moved to GitHub! You find AUGUSTUS for Download at https://github.com/Gaius-Augustus/Augustus. In order to clone the most recent version, type: git clone https://github.com/Gaius-Augustus/Augustus.

  5. bioinf.uni-greifswald.de › webaugustusBioinformatics Web Server - University of Greifswald

    AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. This web server provides an interface for training AUGUSTUS for predicting genes in genomes of novel species. It also enables you to predict genes in a genome sequence with already trained parameters.

    • Katharina J. Hoff
    • 2011

  6. github.com › Gaius-Augustus › AugustusReleases · Gaius-Augustus/Augustus · GitHub

    Genome annotation with AUGUSTUS. Contribute to Gaius-Augustus/Augustus development by creating an account on GitHub.

  7. People also ask

  8. www.ncbi.nlm.nih.gov › pmc › articlesAUGUSTUS: a web server for gene prediction in eukaryotes that ...

    Jul 1, 2005 · We present a WWW server for AUGUSTUS, a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model, a probabilistic model of a sequence and its gene structure. The web server allows the user to impose constraints on the predicted gene structure.