This tool complements the functionality of the ‘Match’ tool when applied to partial rRNA query sequence(s). Use the ‘Proxy’ tool to find probes/primers that potentially target an organism that is only represented by a short rRNA gene read e.g. as obtained by multiplexed amplicon sequencing with next-generation sequencing technologies.
A proxy match finds corresponding near full-length rRNA sequences for short query sequences and matches the long proxy sequences against the oligonucleotides in probeBase analogous to the ‘Match’ tool.
The proxy sequences are retrieved from the small or large subunit rRNA reference database (Ref NR 99 Release 123) of SILVA. The output includes the identified proxy sequences for each partial query sequence and shows the probes or primers that have up to two mismatches to the proxy sequences. The minimal number of proxy sequences (in %) that must be matched by a primer/probe can be selected.
The tool can be tested using the “Load example” button, which pastes example partial 16S rRNA sequences in fasta format into the text field.