Next: Exit Status Codes
Up: primer3
Previous: What to do if
Contents
Also see the file release notes in this directory.
- 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
- 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
- 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)
Next: Exit Status Codes
Up: primer3
Previous: What to do if
Contents
Brant Faircloth
2006-02-15