Question re TEMPLATE_MISPRIMING parameters

primer3-org / primer3

Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).

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Question re TEMPLATE_MISPRIMING parameters #43

Closed genya closed 3 years ago

genya commented 3 years ago

is there a way to restrict the consideration of primer mispriming to a certain number of bases from the 3' end of the primer? In other words, make it so that the PRIMER_MAX_TEMPLATE_MISPRIMING parameter ("The maximum allowed similarity to ectopic sites in the template. ") only takes into account a specified portion of the primer nearest the 3' end. Is that possible?

bioinfo-ut commented 3 years ago

I am not sure. But perhaps Primer3_masker would help you in this case? There you can define k-mer length ("specified portion") that is used for finding binding sites in the template. Primer3_masker: integrating masking of template sequence with primer design software https://github.com/bioinfo-ut/primer3_masker https://academic.oup.com/bioinformatics/article/34/11/1937/4817620