2.3.2. Sequence based query
Three origins for the sequence query are proposed in three distinct tabs
of the submission interface:
Submit your sequence. If the user has a FASTA-formated
barcode sequence that matches the barcode sub-region targeted by the
dataset (eg. the V9 sub-region of the 18S), the first option (eg “18SV9
region”) can be selected. If not, the user can select the second option
(eg “18S complete”) which will extract the corresponding sub-region
from the sequence query with cutadapt version 2.1 software (Martin,
2011).
Search from a ref db sequence. A taxonomic search allows
the user to identify a barcode from a reference database (PR² forTara Oceans OTU 18S-V9 (Guillou et al., 2013) or SILVA release
115 (Quast et al., 2013) for Tara Oceans 16S rRNAmiTags and Malaspina-2010 OTU 16S-V4V5).
Search from an ID. This third tab caters for users with a
list of OTU identifiers to use as queries (the OTU identifiers must
correspond to those used in the original datasets). A “one map
per barcode ” option is available if less than 5 barcodes are selected,
allowing each barcode to be presented on a separate map or bubble plot
in the results panels.
If one of the two first tabs has been used to define the query
(“Submit your sequence ” or “Search from a ref db
sequence ”), an alignment is computed (using VSEARCH) (Rognes et al.,
2016) between the selected barcode query and the OTU sequences of the
selected metabarcode dataset. An optional phylogenetic tree can be built
in order to compare the user barcode query sequence with its homologous
target OTU sequences.