Probe Match FAQ

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Is there a tutorial for how to use probe match?
Yes, you can find one here.

How do I test forward and reverse primers with the database?
Both the forward and reverse primers should be entered as 5'-3'. The difference is the forward primer is on the "+" strand and the reverse primer is on "-" strand of the gene. Therefore, In RDP Probe Match, the forward primer should be set to target '-' strand, while reverse one should be set to target '+' strand.

How do I download the full sequences for the hits I get when doing a probe match?
First, download the hit list from the Probe Match page which can be specified to subgroups. Then, upload the list to 'SeqCart', which makes the selection of the sequences on the downloaded list from the first step. Finally, go to the download page.

Are there any plans for a service that matches both forward and reverse probes concurrently and allows you to view the results by matching ranges?
We will not be able to offer this function online any time soon. However, we would be happy to run your primers against RDP database using a command-line tool to obtain the in-silico PCR information if you send us the primer sequences and specify which group of organisms you are interested in.

Regarding probe match, what kind of search is done on the database?
Probe Match searches the entered text string over the database sequences (not the alignments) using Eugene Myers's Bit-vector algorithm.

What algorithms/settings does RDP use to determine whether sequences are "good" or "suspect"?
RDP uses UCHIME as a quality filter.

Is there a way to do a probe match against sequences I have uploaded?
No, you can only probe match to the database. However, RDP command-line version of Probe Match tool enables you to perform the same function against your own sequences.

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