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The name "MFEprimer" comes from the title of the first paper (2009, Bioinformatics): Multiple Factor Evaluation of the specificity of PCR primers. And both the version 1.0 and version 2.0 (2012, NAR) are only focused on primer specificty, leaving dimers and hairpins for users. However, dimers and hairpins are very important factors affecting success of PCR. So, for version 3.0, we expand the functions of MFEprimer, and make it as a full-functional primer quality control (PrimerQC, maybe the new name) program.
- genomewide specificity check. Allowed mismatch at the 3' end, but exclude the first base at the 3' end. This feature will make MFEprimer more sensitively and accurately, the price is slow.
- new and fast dimer check algorithm;
- new and fast hairpin check algorithm;
- primers compatible check for multiplex PCR;
- thermodynamics based hybridization analysis;
- core algorithm was rewritten with golang, which is fast and parallel.
- Adjust parameters more sensitively for hairpins and dimers.
- Update the thermodynamics calculation for hairpins and dimers.
- Register an account to help you manage your tasks, you won't miss or forget any tasks any more.
- Because of the highly similar of the 16S sequences, MFEprimer may report errors when checking quality of primers against 16S databases (e.g., Bacteria 16S, Fungal 28S and Archaea 16S).