3.1.2. Sequence based query results
Intermediate query selection pages. When the query was submitted via the “Submit your sequence ” and “Submit a ref db sequence ” submission interface (Figure 1), intermediate pages allow users to select which homologous metabarcode sequences to use as queries for the analyses. In the case of submission via the “Submit a ref db sequence ” option, a first intermediate page lists available reference sequences from the PR2 or SILVA databases, including their taxonomic classification and nucleotide sequences, together with radio buttons to select the appropriate query sequence. The query sequence is then aligned (using VSEARCH by default) with OTU sequences from the selected metabarcode dataset. The following intermediate page then lists matching metabarcodes by order of decreasing sequence similarity (limited to the first 500 hits) (Figure 2D). Above the list, a bar chart showing the distribution of alignment percent identities can be used to select which homologs to carry over for analysis. The “one map per barcode ” option is only applicable if less than 5 barcodes are selected, allowing each barcode to be visualized on separate maps and bubble plots.
Result interfaces. The biogeography of the metabarcode sequences homologous to the user query is displayed in the following four interactive panels: geographic distribution (Figure2A), co-variation with environmental variables (Figure 2B and C), taxonomic distribution (Figure 2E) and phylogenetic tree (Figure 2I) if the “Phylogenetic tree ” option was ticked in the initial submission interface (unchecked by default). If the ”Environmental variable filtering ” option is selected on the world map, the user can filter out samples using the provided slider (Figure 3).
Regardless of submission route, the complete set of data necessary to independently re-build each figure is downloadable as flat files from the final results page (namely the list of rDNA hits, the corresponding FASTA formatted sequences, the biosample abundance matrix and the contextual environmental variables).