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Sequence match

Use this tool to find all probes/primers that match your query rRNA sequence(s).

A match of an rRNA sequence against all probes in probeBase recovers all reversely complementary probes. A match of an rRNA sequence against all primers in probeBase recovers all reverse complementary - antisense - primers (i.e. reverse primers) and all sense primers (i.e. forward primers).

Up to 1000 query sequences can be uploaded as fasta file. The maximum number of mismatches of probes/primers with your query sequence(s) can be selected. The output is either a list of oligonucleotides targeting your query sequence(s) or a list of query sequences for which oligonucleotides were found.

A typical application of this tool is to quickly retrieve a set of available FISH probes that target rRNA sequences determined in an environmental microbial diversity survey without the need for extensive comparative sequence analysis. This probe set can then be readily applied for FISH to determine the abundance and spatial organization of the target organism in the sample.

The tool can be tested using the “Load example” button, which pastes example near full length 16S rRNA sequences in fasta format into the text field.

Match rRNA sequence against probe/primer sequences