I'd like to detect DNA encoding for a microbial enzyme in clinical samples via qPCR, independently of bacterial species. Does anyone know of good tool/programme/database to find the conserved regions to be able to design consensus primers?
Or has another good strategy of how to do that?
Thanks a lot!
Even though you are not interested in any species, you need to have knowledge about the species and relationship between them. Also, you must decide for any candidate enzyme/gene which might be conserved throughout bacterial and fungal species.
If you know this information, you can get the gene sequences from any database like NCBI or ENA and do a multiple sequence alignment. Check for any conservation, if any. Do a phylogenetic analysis to check if the alignment and tree makes sense. Since you wanted to design primers for over all species, you might have to design degenerate primers.
- Badges
- Science method