Explore Biosynthetic Gene Clusters

Similarly to the genome table, you can explore the BGCs interactively. More specifically, you can:

  • Click on a BGC to explore the abundance of its family (GCF).
  • Sort a column by clicking on the arrows next to its names.
  • Sort by multiple columns by pressing shift when clicking on an additional column.
  • Search for a word or pattern in the table using a global search with regex enabled. For instance, you can look for Tara genomes with `TARA_`, or use `_METAG_` to select MAGs only or `_REFG_` for reference genomes. MAGs from this study can be queried with `_METAG_[A-Z]{8}` (Excludes Tara MAGs from an other study). To make sure that you only pick up perfect matches, use `$` at the end of the word, e.g. `cluster_1$` will only pick up that cluster and not all numbers starting with 1.
  • Select rows by searching multiple column at once. With regex you can create the desired pattern using double space between columns, so, for instance `TARA_.*;p__Myxococcota;` w ill filter TARA genomes annotated as p__Myxococcota by GTDB ,`MARD_.*c*Actinobacteriota;` will filter MARD genomes annotated as p__Actinobacteriota by GTDB and `MALA_.*;p__Eremiobacterota.*C2$` wi ll filter MALA genomes annotated as p__Eremiobacterota by GTDB belonging to the Species Cluster C2.
  • You can also move down to the search panes for per column and numeric filtering. Note that not all the columns are enabled (usually because they can either be searched or did n ot appear too useful), and they may not provide the best filtering options out of the box: feedback is welcome to improve the user experience.
  • Export a filtered table, or after applying visibility contraints as imposed by the Toggle Columns button or selected rows only with the export button. Prior to any export, sele cted rows should be ticked. To select all rows for export, click the Select All button first.
  • Depending on your computer/browser searching and filtering might take some time. For finer control and reactivity feel free to prefilter/select and export the table to work loc ally.
Biosynthetic Gene Clusters
Select Id BGC Genome Taxonomy bgc_length bgc_complete bgc_representative gcf gcc products Non Ribosomal Peptide Synthetases Type I Polyketide Synthases Type II/III Polyketide Synthases RiPPs (Ribosomal_Natural_Products) Terpenes Other distance_refseq distance_mibig gcc_prevalence gcc_to_refseq gcc_only_mag