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

Question

[gprezza]

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.

[cpad0112]

Not a python solution, But you can try seqkit for locating primer sequence in sequence(s) of interest. without penalty, you can use seqkit for locating pcr primer on forward and reverse strand of your sequences:

$ seqkit locate -p <primer_sequence> <target_sequence(s) in fasta format>

[gprezza]

I need a way to check if my primer could be used as such in the target sequence. For this reason, I need a tool that weighs mismatches based on their location in the primer (i.e. almost ignore the ones in the 5' end), exactly like in-silico PCR tools do. If i get it correctly, seqkit doesn't do that.

[Camp]

Hey, did u find a solution to your problem? I am in a very similar position. I have to run a pair of primers against a bunch of genomes I've been told to try primersearch on Emboss by python script but im finding it quite complicated

Answer 1

[ATpoint]

You could use PrimerBLAST if you have a second primer that is supposed to work with this primer you have. You can then provide PrimerBLAST with the target sequence plus both fwd and rev primer and a background genome, so PrimerBLAST will check if (against that genome) the primer pair is specific to generate the sequence you want. PrimerBlAST is essentially Primer3 (so its scores and metrics) plus BLAST, so pretty much exactly what you need.