Further instructions for your metagenomics report

31 outubro 2017, 14:19 • Rodrigo Costa

Hello everyone,

Here is a summary on how to submit your job to antismash to predict the secondary metabolite biosynthesis potential of your actinobacteria.

In the Antismash webpage (https://antismash.secondarymetabolites.org):

1. Write the e-mail address where you want to get the results;

2. Under “data input”, choose “Upload file”;

3. Browse on your computer the .fasta file obtained from Elviz and click “open”;

4. After step 3, new buttons will appear requesting whether you want to use “Prodigal” or “metagenomes” to analyse your data. Choose “metagenomes”;

5. Under “Analysis Options”, turn “ClusterFinder” and “Use ClusterFinder algorithm for BGC border prediction” on;

6. Keep all other parameters as default and click on “submit”.

 

Please note: you need to send two jobs to antismash. One for the group “Actinobacteria”, containing all contigs belonging to this phylum which could not be classified any further into classes orders etc (634 contigs); and one for the group “Actinomycetales” containing all contigs belonging to the order Actinomycetales (1087 contigs) in the phylum “Actinobacteria”.

 

The results for both groups will contain a long list of “putative” biosynthetic gene clusters (BGCs) and fewer BCGs presenting similarities with those involved in the biosynthesis of known compounds. In your report, you may tell how many BGCs, putative or not, were found in each job, but should focus on two or three interesting BGCs only for discussion.

All the best,

Rodrigo