HTTPS SSH

antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell

Build Status install with bioconda

antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.

External tools

antiSMASH is powered by several open source tools: NCBI BLAST+,HMMer 3, Muscle 3, Glimmer 3, FastTree, TreeGraph 2, Indigo-depict, PySVG and JQuery SVG.

Development & Funding

The development of antiSMASH was started as a collaboration of the Department of Microbial Physiology and Groningen Bioinformatics Centre of the University of Groningen, the Department of Microbiology of the University of Tübingen, and the Department of Bioengineering and Therapeutic Sciences at the University of California, San Francisco. With the move of the PIs and developers, development continues now at the Manchester Institute of Biotechnology, the Bioinformatics Group at Wageningen University and The Novo Nordisk Foundation Center for Biosustainability in Hørsholm.

antiSMASH development was/is supported by the GenBiotics program of the Dutch Technology Foundation (STW), which is the applied-science division of The Netherlands Organisation for Scientific Research (NWO) and the Technology Programme of the Ministry of Economic Affairs (grant STW 10463), GenBioCom program of the German Ministry of Education and Research (BMBF) grant 0315585A, the German Center for Infection Research (DZIF) and the Novo Nordisk Foundation.

Publications

Kai Blin, Marnix H. Medema, Daniyal Kazempour, Michael A. Fischbach, Rainer Breitling, Eriko Takano, & Tilmann Weber (2013): antiSMASH 2.0 — a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Research 41: W204-W212.

Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Rainer Breitling & Eriko Takano (2011). antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Nucleic Acids Research 39: W339-W346.

Installation

Unfortunately, antiSMASH is a bit complicated to install from source, and we recommend using one of the pre-built installers from our download page instead.

Manual installation on Linux

First, make sure you have the following antiSMASH dependencies installed:

  • diamond (version 0.8.36 tested)
  • fasttree (version 2.1.7 tested)
  • glimmer (version 3.02 tested)
  • GlimmerHMM (version 3.0.4 tested)
  • hmmer2 (version 2.3.2 tested, append a 2 to all hmmer2 executables to avoid conflict with hmmer3 executable names, like hmmalign -> hmmalign2)
  • hmmer3 (version 3.1b2 tested)
  • mafft (version 7.271 tested)
  • meme (version 4.11.2 tested. Version 4.11.4 changes output file formats, so don't use that.)
  • muscle (version 3.8.31 tested)
  • NCBI blast+ (version 2.2.31 tested)
  • prodigal (version 2.6.1 tested)
  • xml development headers (version 2.9.1 tested)
  • xz development headers (version 5.1.1 tested)
  • python (version 2.7.9 tested, any python 2.x >= python 2.6 should work)
  • python-virtualenv (not needed, but highly recommended)

Then, create a python virtualenv for installing the antiSMASH python dependencies. This is not required, but highly recommended.

virtualenv as3
source as3/bin/activate

All the python dependencies are listed in requirements.txt, you can grab them all and install them with a simple command:

pip install -r requirements.txt

Last but not least, run download_databases.py to grab and prepare the databases:

python download_databases.py