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).