Differences from Earlier Versions

Also see the file release notes in this directory.

1. Compared to v2
   • Tag name changes. However, Primer3 should understand most or all Primer v2 input tags, and should produce v2-compatible output tag names when the -v2_compat command-line switch is used
   • The one exception is that the PRIMER_RECOMMEND tag is no longer produced. Instead Primer3 produces the PRIMER_x_EXPLAIN output tags. The format of the data in this tags is different from the data in v2's PRIMER_RECOMMEND output tag
   • Numerous fixes.
   • Uses the PRIMER_SELF_ANY and PRIMER_SELF_END parameters to govern maximum allowable complementarity between left and right primers, as well as complementarity between copies of a single oligo or within a single oligo. This behaviour is very close to that of primer 0.5; self complementarity calculations in v2 were unreliable
   • Primer3 produces much more output information, including the TMs and self complementarity measures of selected primers
2. Compared to both v2 and 0.5
   • The format of the contents of .for, .rev (and .int) files is different
   • Primer3 returns a user-specifiable number of primer pairs (or triples) sorted by ``goodness''
   • Primer3 will find a primer pair if any acceptable pair exists
   • Optional n-based indexing into source sequence
   • Use of sequence quality and 3' stability as constraints in primer picking. Optional positional component to objective function
3. Compared to 0.5
   • Completely different input format
   • It has been reported the 0.5 deleted Ns when they occurred in primers
   • More stringent self-complementarity defaults
   • Primer3 selects internal oligos on request (and produces .int files if requested)