Frequently Asked Questions#

Can I run epsSMASH locally as a stand-alone program?#

Yes. A stand-alone version of epsSMASH is available on GitHub. Please see the Install Guide for instructions on how to install and run it.

Why doesn't epsSMASH detect my gene cluster?#

Some exoPS gene clusters may not be detected by a strict or relaxed rule and thus will only be given a generic name such as "wzy_dependent_putative" by one of the loose rules (see rules hierarchy). If epsSMASH detects your gene cluster like this and you believe it should be detected by a more specific rule, please contact us. If you are aware of a true exoPS biosynthesis gene cluster that escapes any detection by epsSMASH, please contact us, and we will add the models necessary to detect it.

In some cases, two or three gene clusters appear to be fused into one gene cluster by epsSMASH while they are in fact separate gene clusters. Why is this?#

Currently, it is not possible to judge on the basis of sequence information only whether a large cluster of secondary metabolite biosynthesis genes of different types is either a hybrid gene cluster or comprises multiple separate gene clusters that are located very close to one another. A careful manual study of the provided comparative gene cluster analysis results may provide hints on solving this question.

Why are several genes upstream and downstream of gene clusters included, even though they do not seem to be part of the gene cluster?#

We try to be very conservative in cutting gene cluster borders, leaving this to the expert eye of the user, as it is better to show some extra genes than to leave out key genes.

Can I also submit an unannotated genome sequence in FASTA format?#

Yes. We offer integrated preliminary gene prediction by Prodigal based on a FASTA input. You can also upload annotations in GFF3 format.

What is the privacy policy of epsSMASH concerning my sequence data?#

We try to keep this site and the data that it analyzes as safe and secure as possible. Your output files will be deleted from our server within one month. However, sending your data to the web site is at your own risk. If you are concerned about the sensitivity of your data, please use the stand-alone version of our tool.