I'm trying to check the primers and probe design from a paper. I'm using primer-BLAST to do so for the primers, but I'm not sure how to check the probe sequences.
I would recommend using IDT's Primer Quest tool, it is far superior to Primer-Blast and you can design for probe detection.
https://www.idtdna.com/PrimerQuest/Home/Index
then blast the sequences blastn tool, just change the database to genomic + transcript and then choose your species
If you want to check the probe sequence position within targeted genome sequences you can just blast it in blastn: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
Alternatively, you can use BioEdit and the search option to check the probe sequence positions.
If you are looking for online tools to design TaqMan PCR sets, for example, you can check:
https://www.genscript.com/tools/real-time-pcr-taqman-primer-design-tool
https://eurofinsgenomics.eu/en/ecom/tools/qpcr-assay-design/
Check https://www.idtdna.com/pages/education/decoded/article/designing-pcr-primers-and-probes
https://www.idtdna.com/pages/education/decoded/article/designing-pcr-primers-and-probes
Also check https://pubmed.ncbi.nlm.nih.gov/25697650/
https://www.bio-rad.com/en-us/applications-technologies/qpcr-assay-design-optimization?ID=LUSO7RIVK
Use the following procedure
https://www.intechopen.com/chapters/65252
https://eurofinsgenomics.eu/en/ecom/tools/qpcr-assay-design/
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