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primer3-org / primer3

Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).
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What PRIMER_PRODUCT_OPT_SIZE is needed for? #67

Closed DmitriiSukhomlinov closed 2 years ago

DmitriiSukhomlinov commented 2 years ago

How should I use PRIMER_PRODUCT_OPT_SIZE? Is that the same as PRIMER_OPT_SIZE or have some difference? Reading the manual I've got a suggestion, that it's kinda an optimum size for Penalty Weights for Primer Pairs, but I'm not clearly sure. Also, why is this parameter isn't presented into a Web version of Primer3?

untergasser commented 2 years ago

You should not use PRIMER_PRODUCT_OPT_SIZE as it makes calculations very slow. You can define the exact length of the product with this tag. You should use the ranges instead: PRIMER_PRODUCT_SIZE_RANGE.

PRIMER_OPT_SIZE gives the optimal size of a primer.

As PRIMER_PRODUCT_OPT_SIZE slows down calculations dramatically, it is not accessible via the web interface.

Best,

Andreas

DmitriiSukhomlinov commented 2 years ago

Thank you so much, I got it