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release 1.0a 9/06 ==================================================
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No new functionality (bug fixes and minor code cleanup only)
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* Corrected calculation of ..._TEMPLATE_MISPRIMING when
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INCLUDED_REGION was set (thanks to Tomoaki Nishiyama, Advanced
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Sciences Research Center, Kanazawa University, Japan).
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* Corrected error that caused crash when
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PRIMER_WT_TEMPLATE_MISPRIMING was set (thanks to Peng Yu,
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Functional Genomics Group II, Chinese National Human Genome
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* Added olgiotm_main.c (for executable oligotm)
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release 1.0 6/04 ==================================================
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Added ability to search source sequence (template) for
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mispriming or mishybing sites.
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Added _experimental_ facility to calculate Tm on long
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oligos using a GC% based formula.
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Miscellaneous fixes and cleanup, including:
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* Avoiding closing NULL file handles when a mispriming or mishyb
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* Correction to long_seq_tm() in oligotm.c plus addition of
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* Gave user the ability to _not_ treat IUB/IUPAC ambiguity
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codes as a consensus while matching against mispriming
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or mishyb libraries. Inability to turn off this "feature"
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caused severe problems when libraries contained strings
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of N's: NNNNNNNNN, since if N is treated as a consensus,
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release 0.9 9/98 ==================================================
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Corrected errors in calculation of amplicon Tm.
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release 0.8 6/98 ==================================================
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Added flexible objective function. Various tags governing
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the penalty weights are not fully documented in this
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Added much changed web interface.
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Added ability to select only a single
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left or right primer or hyb probe.
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Made it possible to continue even if
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PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_INPUT is
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Added PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_GC_PERCENT
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release 0.7 5/98 ==================================================
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Fixed the 'case problem' for
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PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_INPUT (and at the
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same time a related bug).
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Added experimental PRIMER_START_CODON_POSITION tag
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and related outputs. This feature should still be
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considered experimental and the user should scrutinize
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Added PRIMER_PRODUCT_{MAX,MIN}_TM and related outputs.
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release 0.6 ==================================================
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Bug fixes (most introduced as part of 0.5 enhancements).
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release 0.5 ==================================================
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** Non-Backward compatible change:
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Fixed inconsistency in output format;
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PRIMER_INTERNAL_n_OLIGO_SEQUENCE
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-> PRIMER_INTERNAL_OLIGO_n_SEQUENCE.
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The old format can be preserved by
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compiling with the precompiler
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symbol USE_OLD_FORMAT_MISTAKE defined.
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Added end-anchored local alignment option to dpal.
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Removed some un-needed dpal implementations.
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Added end-anchored local alignments for checking
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Added mispriming estimates for primer _pairs_
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(see PRIMER_PAIR_MISPRIMING_LIBRARY),
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with related new output tags. Trivial change
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in maximum allowable library sequence weight.
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Added an experimental primer position component to
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the objective function (PRIMER_{IN,OUT}SIDE_PENALTY),
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with related new output tags.
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Added sequence quality scores as constraints
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in primer picking (PRIMER_MIN_{,END_}_QUALITY,
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PRIMER_QUALITY_RANGE_{MIN,MAX}) with related
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Added more error reporting to primer3.cgi when primer3
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exits with a non-0 termination status.
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Fixed bug when non-0, non-1 value was supplied
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for pick internal oligos.
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Added PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_INPUT
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for checking or for designing around existing primers or
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Added error checking for duplicates of certain
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tags, such as SEQUENCE.
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Added PRIMER_MAX_END_STABILITY and related changes
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release 0.4b ==================================================
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Corrected bug in parsing of INCLUDED_REGION tag.
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release 0.4 ==================================================
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Added optional check of oligos against "mispriming" or
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"mishyb" libraries with related changes to formated output
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and to the contents of primer list files.
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Modified search algorithm to compute complementarity/
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similarity measures as late as possible.
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Got rid of quotes (") around error and warning strings.
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Fixed numerical overflow on input sequences longer than
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MAX_SHRT. (Thanks to Pete Young for finding this one.)
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release 0.3 ==================================================
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Changes to dpal to make it substantially faster on the maxgap=1
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case for local and end-anchored complementarity measures.
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Removed restriction on maximum sequence length (by removing
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ftar, fexcl, fexcl_int, fnn, fn, fgc arrays, which necessitated
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internal changes to methods for calculating overlap with
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excluded regions and targets and to calculate spanning of
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Modified 'primer list' format (clean up and hopefully got rid
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of spurious regression test discrepancy on some systems due to
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differences in rounding).
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Exit codes for some errors changed.
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Text of error messages for PRIMER_PRODUCT_SIZE -> PRIMER_PRODUCT_SIZE_RANGE.
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Some errors that should have been global (fatal) were not.
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These were fixed and error handling rationalized somewhat.
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An error in the display of the start position of targets, and
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excluded regions in formated output was corrected.
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An error in which overlapping product size ranges caused
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primer3 to return duplicate primer pairs was corrected.
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Made regression tests more complete.
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Made the maximum number of primer pairs to return a
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parameter (PRIMER_NUM_RETURN).
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Added optional n-based indexing in input and output
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(PRIMER_FIRST_BASE_INDEX=n). Has not been tested
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release 0.2b (10/11/96) ==================================================
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Added PRIMER_WARNING tag.
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Made it legal for excluded regions and targets to lie outside
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of included region. Documentation fixes (especially to
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release 0.2a ==================================================
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Tweaks to formated output to make it more complete
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(included complementarity measures); adjusted tests.
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release 0.2 ==================================================
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Made 0-length excluded region legal, and adjusted tests.
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Tweaked error reporting of negative-length excluded regions,
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internal oligo excluded regions, and target.
added
removed
src/release_notes.txt
