Minnesota Supercomputing Institute
With regards to the safety measures put in place by the university to mitigate the risks of the COVID-19 virus, at this time all MSI systems will remain operational and can be accessed remotely as usual. The only planned outages concern our in-person Helpdesk and tutorials. More information, as well as alternative remote support options, can be found at MSI COVID-19 Continuity Plan
Thursday, August 2, 2018
From the web site:
The secondary metabolism of bacteria and fungi constitutes a rich source of bioactive compounds of potential pharmaceutical value, comprising biosynthetic pathways of many chemicals that have been and are being utilized as e.g. antibiotics, cholesterol-lowering drugs or antitumor drugs.
Interestingly, the genes encoding the biosynthetic pathway responsible for the production of such a secondary metabolite are very often spatially clustered together at a certain position on the chromosome; such a compendium of genes is referred to as a 'secondary metabolite biosynthesis gene cluster'.
This genetic architecture has opened up the possibility for straightforward detection of secondary metabolite biosynthesis pathways by locating their gene clusters. In recent years, the costs of sequencing bacterial and fungi has dropped dramatically, and many genome sequences have become available. Based on profile hidden Markov models of genes that are specific for certain types of gene clusters, antiSMASH is able to accurately identify the gene clusters encoding secondary metabolites of all known broad chemical classes.
antiSMASH not only detects the gene clusters, but also offers detailed sequence analysis.
The antiSMASH application cannot be run as a loaded module. It must be installed and run from local user space.
An antiSMASH install script is available on the MSI Lab cluster, Itasca and Mesabi.
Steps for a local installation:
1) Login to MSI Lab cluster, Itasca orMesabi.
2) Create an install directory within your local directory (for instance /home/YOUR_GROUP/YOUR_USER_NAME/antiSMASH)
3) CD to the directory created in step 2 and run the following command:
This command will load modules, download and untar code, download and prepare needed databases all within the directory created in step 2. The install will take a few minutes.
4) To run, put the 'run_antismash_wrapper' script into your path.
Do not call run_antismash.py directly. Use the wrapper since it invokes the virtaul environment.
4) The command
will provide a list of available antiSMASH commands.
Help documentation is available from the antiSMASH web site.