Understanding ARTS results

The goals of this tool are to automate the process of performing target direct genome mining (TDGM); search for potential novel antibiotic targets, and prioritize putative secondary metabolite gene clusters.

There are three fundamental ARTS criteria for TDGM as listed below:

• Proximity check: Cross reference locations with Secondary Metabolite gene clusters. For more information about BGC prediction, please visit antiSMASH help page
• Uncommon duplication check: Highlight potential repurposed primary metabolism genes
• Phylogenetic incongruence: Highlight essential genes with evidence of inter-genus horizontal transfer

Please visit ARTS help page for more information.

Selection of genome pool and ARTS criterion

1- First select the genome pool for querying. Click on Antismash DB for high quality genome assemblies from NCBI also present in antismash DB or click on Earth Metagenomes option for mining metagenome assembled genomes described by Nayfach et.al., 2020 Nature Biotechnology.

2- Select one of the fundamental ARTS criteria for specialized queries. Note that you can search for HGT evidence via selecting respective search option from "Core Hits" or "Summary Results".

3- After selecting main categories, add available search option terms of your choice and provide a string (e.g. streptomyces) or a substring (e.g. strepto) to query the database.

Exploring results

1- Your applied query will lead you to a result page, consisting of a dynamic table where you can search for your specific keywords throughout the table, download your selection or navigate to other databases clicking on provided linkouts shown in blue text.

2- Links from: "Assembly id" column will take you to the corresponding ARTS result of given genome, "Cluster" column to the antiSMASH result page, "Model Name" to the phylogenetical and statistical information about selected model throughout ARTS-db and "Bigfam GCF" to the associated Gene Cluster Family via BiGFAM-db.

Querying Potential Targets

Here you can provide a substring of gene description and select a gene (classified from TIGRFAM models) from suggestions. If you have any specific models in mind (e.g.:TIGR00131), you can also pass that as a query and if the model exists in ARTS-DB, you will be directed to the result page.

Target-oriented result page ( Example) consists of phylogenetical and statistical information about the selected gene in terms of ARTS criteria hits such as:

• Distribution of BGC Proximity Hits: Here you can investigate target genes affinity to be proximate to certain types of biosynthetic gene clusters or the taxonomic distribution of resulting BGC proximity hits for that gene.
• Distribution of Duplication Hits: Here the duplication rates of the selected gene with respect to a specific phylum can be investigated. This is also important for BGC expression studies since repurposing primary metabolites can help boost secondary metabolite production.
• Phylogenetic Distribution of target gene with Multiple ARTS Hits: Here you can investigate your targets affinity to be a likely target for a resistance mechanism in corresponding phyla. Please note that these plots are generated for presenting a broader sense of the "resistance potential" of gene of interest. Further investigation should be done by executing specific queries in order to narrow down potential targets in accordance with your current research.
• External Resources: Here you can further check the linkouts to investigate your gene of interests affiliation with databases such as Drugbank or Mibig.

Shaping your search

1- Using "Summary Results" option, it is possible to do an initial filtering of genomes with specific characteristics. As seen in example above, we have limited genomes which have at least 100 core genes and 2 different BGCS, "thermo" in their phylum name and minimum amount of 2 targets that have +3 fundamental ARTS hits, 10 targets which are in proximity of a BGC.

2- Individual ARTS results can be accessed through links in "Assembly id" column for further and closer inspection.

Shaping your search

1- Above example shows how to perform a rather extensive search in the ARTS database. The query itself is pretty self explanatory but to summarize, here we are searching for all the core genes that are in any organism that has "coelicolor" in their name with "protein synthesis" functions and are duplicated, OR (please mind that in search options one box is selected as "Or" operator), the core genes in genus "burkholderia" within proximity of a BGC and annotated as a known resistance model.

2- If you are interested in specific keyword (here, "arginine") in the resulting table, the table can easily be filtered by typing "arginine" to the search box.