release 1.1.3 2008-02-21 ================================================ "Maintenance" release: Corrected overflow of static buffer in boulder_print_pairs() and boulder_print_oligos() in primer3_main.c release 1.1.2 2007-06-10 ================================================ Updates to dpal.c so that no error forces an exit. Adpatation in primer3_main.c and ntdpal_main.c to updated error handling in dpal(). Arranged for primer3_main.c align() to check for and circumvent local alignments to "targets" < 3 nucleotides long, and added tests for this condition. Comment and code readability updates in dpal.h and dpal.c release 1.1.1 3/37/2007 ================================================== Minor corrections release 1.1.0 1/17/2007 ================================================== Added tags PRIMER_TM_SANTALUCIA, PRIMER_SALT_CORRECTIONS, PRIMER_LOWERCASE_MASKING, PRIMER_DIVALENT_CONC, and PRIMER_DNTP_CONC. See the README for details of what these tags do. Briefly, the first two tags allow the use of modern melting temperature calculations. New tests for this functionality were added to the tests/ subdirectory NOTE: The oligotm executable now takes additional arguments. Cleaned up Makefile, and created Makefile for the test directory with a target to clean up after tests Most (but not all) temporary files created by the tests now end in .tmp or .tmp2 Tried to create more informative test for MAX_PRIMER_LENGTH > DPAL_MAX_ALIGN in primer3_main.c NOTE: The oligtotm() function is now provided as a library, liboligotm. NOTE: non-backward compatible change: removed support of flag -2x_compat. release 1.0.1 11/06 ================================================== Identical to 1.0b except for release number release 1.0b 11/06 ================================================== Corrected bug involving check for template mispriming Minor code cleanup release 1.0a 9/06 ================================================== No new functionality (bug fixes and minor code cleanup only) Bug fixes: * Corrected calculation of ..._TEMPLATE_MISPRIMING when INCLUDED_REGION was set (thanks to Tomoaki Nishiyama, Advanced Sciences Research Center, Kanazawa University, Japan). * Corrected error that caused crash when PRIMER_WT_TEMPLATE_MISPRIMING was set (thanks to Peng Yu, Functional Genomics Group II, Chinese National Human Genome Center, Beijing). * Added olgiotm_main.c (for executable oligotm) release 1.0 6/04 ================================================== Added ability to search source sequence (template) for mispriming or mishybing sites. Added _experimental_ facility to calculate Tm on long oligos using a GC% based formula. Miscellaneous fixes and cleanup, including: * Avoiding closing NULL file handles when a mispriming or mishyb library is missing * Correction to long_seq_tm() in oligotm.c plus addition of related tests. * Gave user the ability to _not_ treat IUB/IUPAC ambiguity codes as a consensus while matching against mispriming or mishyb libraries. Inability to turn off this "feature" caused severe problems when libraries contained strings of N's: NNNNNNNNN, since if N is treated as a consensus, any base matches. release 0.9 9/98 ================================================== Corrected errors in calculation of amplicon Tm. release 0.8 6/98 ================================================== Added flexible objective function. Various tags governing the penalty weights are not fully documented in this release. Added much changed web interface. Added ability to select only a single left or right primer or hyb probe. Made it possible to continue even if PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_INPUT is not legal. Added PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_GC_PERCENT output tags. release 0.7 5/98 ================================================== Fixed the 'case problem' for PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_INPUT (and at the same time a related bug). Added experimental PRIMER_START_CODON_POSITION tag and related outputs. This feature should still be considered experimental and the user should scrutinize the output. Added PRIMER_PRODUCT_{MAX,MIN}_TM and related outputs. release 0.6 ================================================== Bug fixes (most introduced as part of 0.5 enhancements). release 0.5 ================================================== ** Non-Backward compatible change: Fixed inconsistency in output format; PRIMER_INTERNAL_n_OLIGO_SEQUENCE -> PRIMER_INTERNAL_OLIGO_n_SEQUENCE. The old format can be preserved by compiling with the precompiler symbol USE_OLD_FORMAT_MISTAKE defined. Added end-anchored local alignment option to dpal. Removed some un-needed dpal implementations. Added end-anchored local alignments for checking mispriming libraries. Added mispriming estimates for primer _pairs_ (see PRIMER_PAIR_MISPRIMING_LIBRARY), with related new output tags. Trivial change in maximum allowable library sequence weight. Added an experimental primer position component to the objective function (PRIMER_{IN,OUT}SIDE_PENALTY), with related new output tags. Added sequence quality scores as constraints in primer picking (PRIMER_MIN_{,END_}_QUALITY, PRIMER_QUALITY_RANGE_{MIN,MAX}) with related new output tags. Added more error reporting to primer3.cgi when primer3 exits with a non-0 termination status. Fixed bug when non-0, non-1 value was supplied for pick internal oligos. Added PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_INPUT for checking or for designing around existing primers or internal oligos. Added error checking for duplicates of certain tags, such as SEQUENCE. Added PRIMER_MAX_END_STABILITY and related changes to output. release 0.4b ================================================== Corrected bug in parsing of INCLUDED_REGION tag. release 0.4 ================================================== Added optional check of oligos against "mispriming" or "mishyb" libraries with related changes to formated output and to the contents of primer list files. Modified search algorithm to compute complementarity/ similarity measures as late as possible. Got rid of quotes (") around error and warning strings. Fixed numerical overflow on input sequences longer than MAX_SHRT. (Thanks to Pete Young for finding this one.) release 0.3 ================================================== Changes to dpal to make it substantially faster on the maxgap=1 case for local and end-anchored complementarity measures. Removed restriction on maximum sequence length (by removing ftar, fexcl, fexcl_int, fnn, fn, fgc arrays, which necessitated internal changes to methods for calculating overlap with excluded regions and targets and to calculate spanning of targets. Modified 'primer list' format (clean up and hopefully got rid of spurious regression test discrepancy on some systems due to differences in rounding). Exit codes for some errors changed. Text of error messages for PRIMER_PRODUCT_SIZE -> PRIMER_PRODUCT_SIZE_RANGE. Some errors that should have been global (fatal) were not. These were fixed and error handling rationalized somewhat. An error in the display of the start position of targets, and excluded regions in formated output was corrected. An error in which overlapping product size ranges caused primer3 to return duplicate primer pairs was corrected. Made regression tests more complete. Made the maximum number of primer pairs to return a parameter (PRIMER_NUM_RETURN). Added optional n-based indexing in input and output (PRIMER_FIRST_BASE_INDEX=n). Has not been tested for n < 0. release 0.2b (10/11/96) ================================================== Added PRIMER_WARNING tag. Made it legal for excluded regions and targets to lie outside of included region. Documentation fixes (especially to PRIMER_DNA_CONC). release 0.2a ================================================== Tweaks to formated output to make it more complete (included complementarity measures); adjusted tests. release 0.2 ================================================== Made 0-length excluded region legal, and adjusted tests. Tweaked error reporting of negative-length excluded regions, internal oligo excluded regions, and target. ============================================================== ============================================================== Compared to non-primer3 progenitors: Compared to primer 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). Compared to both primer 0.5 and primer v2 --------------------------- 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 primer 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.