Search if a single primer could bind to multiple sequences with Python

Search if a single primer could bind to multiple sequences with Python

1

Hi all,

I have one primer and a list of sequences. I want to check to which of the sequences (if any) the primer could bind to. It’s like an in-silico PCR (so mismatches should be more penalized at the 3′ end of the primer than at the 5′ one etc.), but with only one primer.

I can’t seem to find a tool that accepts only one primer instead of a pair. Anyone has any suggestion? Possibly, I would like to integrate this tool in a Python script.


python


primer


primer extension


alignment

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