A Tool to Detect Plant Metabolic Gene Clusters

Frequently Asked Questions

What are hybrid gene clusters?

In your results you might find "hybrid gene clusters". These are metabolic gene clusters that contain all the marker enzymes of at least two classes of metabolic gene cluster.

Can I search for tandem repeat clusters?

Tandem repeat cluster are groups of duplicated genes adjacent to each other. Phytoclust can also be used to search for them. After choosing or uploading your genome of interest, you can chose "Create your own gene cluster rule (combine up to 4 secondary metabolism enzymes families)" and select your enzyme family of interest several times. If you select it twice, the program will search for all occurrences with at least two members of the enzyme family in the given proximity; if you select three, the program will search for all occurrences with at least three members, respectively.

How can I analyse genomes that are larger than the maximum upload size of 1.5 GB?

If your genome of interest is larger than 1.5 GB you can try to either upload the genome chromosome by chromosome if you want to search the entire genome or if you are interested in a particular region you can just upload the sequence of particular interest.

Why do I get "No secondary metabolite clusters were found in the input sequence(s)" in my results?

This message might have several reasons. One reason might be that the sequence you were analyzing does not contain the enzyme families that you searched for or the cluster range and cluster proximity values were chosen too low. Try again with less enzyme families or higher cluster range and cluster proximity values.

Why do I get "No results" as the latest status of the analysis?

The message usually occurs if the uploaded genome assembly is not sufficient high quality.

What is in the download folder?

The folder is zipped and contain an index file that can be opened in any browser to see the results as they are presented on the webpage. (Make sure the download folder is complete for accurate display of the data.) Moreover the putative gene clusters are listed in a .xls table and .gbk file of the individual cluster candidates are available for further inspection.