apachecgibioinformaticsprimer3

primer3 web error , Unrecognized tag, primer3_core Unrecognized tag

I tried to run a primer3 web on localhost , but there was an error on the output when the pick primer.

Primer3 Output:

Unrecognized tag: PRIMER_THERMODYNAMIC_ALIGNMENT=1 ./primer3_core: Unrecognized tag: PRIMER_THERMODYNAMIC_ALIGNMENT=1

INPUT PROBLEM: Unrecognized tag: PRIMER_THERMODYNAMIC_ALIGNMENT=1

(primer3_results.cgi release 3.0.0)

Solution

  • It seems that they eliminated the param PRIMER_THERMODYNAMIC_ALIGNMENT. Now you should use either PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT or PRIMER_THERMODYNAMIC_TEMPLATE_ALIGNMENT. Take a look at the following link:

    http://primer3.sourceforge.net/primer3_manual.htm

    Section "5. CHANGES FROM VERSION 2.2.3". I suppose you use a new version greater than 2.2.3 which has the new arguments.