MFEprimer is a PCR primer quality evaluation and multiplex PCR primer design platform developed by iGeneTech Bioscience. Candidate primers are designed and evaluated against genomic or transcript databases and then checked to avoid primer dimerization. A graphical extension algorithm derived from the core algorithm is used to determine the best primer set combinations (PSC, Primer Set Combinations) for multiplex PCR assays. In addition, the software provides virtual e-pictures to help the users select the best PSC. Experiments from 2X to 5X plex PCR have proven the reliability of the software.
Binding sites searching is more sensitive by updating the k-mer algorithm to allow mismatches within the k-mer except the first base at the 3' end. The binding sites of each primer with stable 3' end are also listed in output.
Command-line version has an option of JSON output to make MFEprimer more useful by acting as a quality control step in "primer design > quality control > redesign" pipeline.
Function of checking whether the binding sites contain SNPs, which will affect the consistency of binding efficiency among different samples.
Try MFE primer now: https://mfeprimer3.igenetech.com/
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