Development news


  1. Bug fixed: remove blank lines in “-inFile” for indexing.


  1. Improvement: use -mismatch flag to indicate mismatch option for kmer and its binding sites. Previous description is not clear. Thanks Dr. Quanwei Zhang.


  1. Bug fixed: use coordinates to filter repeat amplicons. Thanks Dr. Quanwei Zhang.


  1. Notice: new online server is available:


  1. Notice: the database drive was broken, we are trying to fix it, please use server 1#.


  1. Enhancement2# server available hosted by Xiaolei Wang and Dr. Dongsheng Zhao.


  1. Thanks: thanks iGeneTech for hosting MFEprimer-3.0 web server, which requires a large storage disk and computing power.
  2. Notice: now, web site is the main site for hosting documents related PCR primers design and quality control (specificity, dimers, hairpins, and so on).


  1. Bug fixed: unusual bugs when calculating mismatch thermodynamics.


  1. Enhancement: the function of combined databases is back. It is common to check primers against “genome + rna” at the same time to evaluate primers for gene expression. In theory, there is no limit on the databases for combination, if you have any ideas about database combination, please let me know.


  1. Enhancement: more clear messages for tasks.


  1. Bug fixed: web page crashed when no amplicons found.
  2. New feature: 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.
  3. Security: limit the product max size <= 50,000 bp.


  1. Bug fixed: degenerate primers can’t recognize correctly.
  2. Enhancement: allow single primer sequence for quality check.
  3. Enhancement: show the dangerous amplicons count. [amplicons highlighted in red are the ones which have thermodynamics features close to the target amplicon and could be probably amplified in the PCR.]
  4. Bug fixed: can’t recognize lowercase primer sequences.


  1. Bug fixed: database count bug fixed


  1. Enhancement: in addition tofasta format, input primers now supports sequence-only format. MFEprimer will add an unique primer name like “p1, p2, etc.” to name each primer sequences.

    Input format 1: fasta format. The main purpose of this format is to help users to name each primers. The characters after “>” is the name of this fasta record.

    Input format 2: sequence-only format

Hybrid formats are also worked now.



  1. Enhancement: truncate the amplication name when it’s too long to show on a page


  1. Bug fixed: the completed task should not be editable.
  2. Enhancement: give detailed error information for user input.


  1. Enhancement: add download link to let users download the complete MFEprimer result in text format (compressed with gzip) which can be opened with “nodepad++” in Windows and Sublimetext in Mac or Linux.
  2. Bug fixed: Now, the web page will only show the first 100 predict amplicons (if >100) to avoid server crashed. In some cases, especially when evaluate primers against 16S DNA sequences, probably there will be >1000 amplicons. For the whole result, please download the text format.
  3. Enhancement: updated the doc pages.


  1. Enhancement: database list view with bootstrap panel.
  2. Enhancement: amplicons highlighted in red are the ones which have thermodynamics features close to the target amplicon and could be probably amplified in the PCR. 


  1. Enhancement: task view and pagination.


  1. Bug fixed: multiple output primer align diagram.
  2. Enhancement: Output primer Tm and Dg value, assuming they binging their complement sequence.