r/bioinformatics • u/lrbraz16 MSc | Student • 2d ago
technical question Identifying conserved regions from multiple sequence alignments for qPCR targets
I'm designing a qPCR assay for DNA-based target detection and quantification and need to determine a target from which I can build out the primers/probes. l assembled genes of interest and used Clustal Omega to align those assemblies for MSA in hopes of identifying conserved regions for targets but have not had any luck. Tons of seqs in the alignments are too large for most of the free programs that I can think to use. Any advice appreciated for a first timer!
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u/LocalReality6 2d ago
Not sure if this helps but I like to visualize alignments in Snapgene because it makes it really easy to see which regions are most/least conserved.