Version change log
Version v3.6.1 (14-NOV-22)
Implementation of improvement, that now treats ambiguous DNA sequences in the Golden Gate/Type IIs Recognition Sequence (e.g. GAAGNNNNNNTAC for BarI) properly when searching for them.
Version v3.6.0 (07-JUL-22)
Implementation of new feature - j5 parameter PREFERRED_OVERHANG_SEQS - that enables the user to specify a list of overhang DNA sequences to choose preferentially when j5 is selecting from multiple prospective overhangs.
Version v3.5.5 (21-DEC-21)
Minor bug fixes for Genbank input files with overly long label fields with commas or translation fields with spaces. Fixes downstream bioperl-specific Genbank file parsing issue.
Version v3.5.4 (06-DEC-21)
Minor bug fix in determination of when to add PAGE purification cost to an oligo, in the process of cost optimizing the DNA assembly strategy.
Version v3.5.3 (01-OCT-21)
Minor changes to regex patterns and proximal code that seek to identify the highest numbered master plasmid, oligo, direct synthesis input by the user. No impact on results, but eliminates some unhelpful warning messages.
Version 3.5.2 (15-JUL-21)
Minor change that prevents a DNA synthesis fragment from thinking that it contains the same target part more than once.
Version v3.5.1 (11-JUN-21)
Minor bug fix for importing/processing GenBank files with ? (question mark) characters in feature labels.
Version 3.5.0 (09-JUN-21)
Implementation of a feature that enables a user to specify/override the name (i.e. display ID) that j5 uses to refer to a source sequence. Implementation of a feature that enables a user to specify a URL associated with a source sequence.
Version 3.4.6 (15-MAR-21)
Minor change for situation in which the username is undefined. Minor bug fix in distributing pcr reactions, when assembly pieces derived from Direct Synthesis/PCR were not being treated like PCR-derived assembly pieces, from the standpoint of needing to set up more PCR reactions when a given reaction is for an assembly piece used many times.
Version 3.4.5 (23-FEB-21)
Minor bug fix for downstream automation, erroring out when trying to load multi-well plates with well names (e.g. A13) that do not exist given the number of columns (e.g. 12) and rows (e.g. 8) specified in the downstream automation parameters file. This happens when a user is trying to load a 384-well plate, for example, when the parameters are specifying the use of 96-well plates.
Version 3.4.3 (21-AUG-20)
Minor bug fix to correctly generate assembled sequences for mock assembly designs including EMPTY parts.
Version 3.4.2 (14-AUG-20)
Minor bug fix concerning not trying to update internal preferred overhangs/overlaps for EMPTY parts.
Version 3.4.1 (06-AUG-20)
Minor bug fix concerning the verification of Eugene rules needing to account for EMPTY parts in a combinatorial setting.
Version 3.4.0 (05-AUG-20)
Important update, implementing EMPTY parts in both single and combinatorial design modes.
Version 3.3.9 (10-JAN-20)
Replacing md5_hex hashing with sha256_hex hashing.
Version 3.3.8 (02-DEC-19)
First implementation of maximum DNA synthesis length constraint via j5 parameter setting.
Version 3.3.7 (30-AUG-19)
Changes now requiring j5 user accounts for SBOL Converter tool (either via perl-cgi simplified interface or via XML-RPC). Fix for bug that did not properly check if a timestamp was well defined before creating/cleaning up temporary working directories.
Version 3.3.6 (4-Jun-19)
Minor bug fix for Distribute PCR Reactions functionality when a particular thermocycler zone contains no PCR reactions.
Version 3.3.5 (21-Feb-19)
Minor update including fix for Annealed Oligos naming - removing superfluous flanking parentheses.
Version 3.3.4 (26-Oct-18)
Implemented new feature and minor performance enhancement. New feature is the addition of a j5 parameter (MINIMUMDNASYNTHESISLENGTHBPS) that sets the minimum DNA synthesis length. This parameter must be set greater than the minimum PCR reaction size (MINIMUMPCRPRODUCTBPS), since synthetic fragments are designed to be re-amplified prior to assembly, or it will automatically get set to be as big as the minimum PCR reaction size. In the event that a particular target part is forcibly set to a "Direct Synthesis" assembly strategy, or needs to be synthesized because it can not fit into a primer and is too small to be PCR'd, for example, j5 will attempt to extend the DNA synthesis to at least the minimum DNA synthesis length. If it is unable to do so, if the user originally forced the "Direct Synthesis" assembly strategy, j5 will reset the assembly strategy and attempt to find a viable alternative (e.g. embed in a primer or PCR). However, if the target part otherwise needed to be synthesized, j5 will not have an alternative and will exit with an error message. The minor performance enhancement includes storing Blast/Primer3 lookup table keys as hashes to save memory and expedite look-ups.
Version 3.3.3 (19-Oct-18)
Further performance improvements, and new downstream automation functionality. Performance improvements - these derive from: 1) only reading in/defining parts once per combinatorial design, and 2) only processing sequence objects containing feature annotations during the final sequence assembly of each construct (otherwise only using sequence objects without feature annotations), since feature annotations do not affect other parts of the assembly design process. New downstream automation functionality - these are for the downstream (split and pool) distribute PCR reactions functionality, in which now a new downstream automations parameter ASSEMBLYREACTIONSPERPCRREACTION dictates when a give (split and pool) PCR reaction will be duplicated because it is generating an assembly piece that will be used across multiple assembly reactions [for example - if ASSEMBLYREACTIONSPERPCRREACTION is set to 5, and the same assembly piece will be used across 6 assembly reactions, the PCR reaction generating the assembly piece will be duplicated once so that there is enough of the assembly piece (PCR reaction product) to be used in the 6 assembly reactions].
Version 3.3.2 (09-Oct-18)
Implemented a performance enhancement, in which bl2seq (pairwise blast) and Primer3 primer designs are cached, so that they may be looked up rather than re-calculated (rather than having to make expensive calls to bl2seq or Primer3 again).
Version 3.3.1 (04-Oct-18)
Implemented a performance enhancement, in which Primer3 Tm calculations are cached, so that they may be looked up rather than re-calculated (rather than having to make expensive calls to Primer3 again).
Version 3.3.0 (31-Aug-18)
Several substantial changes and bug fixes. In terms of changes affecting performance (benefits): 1) for combinatorial designs, only reading in master sequences, plasmids, oligos, and direct syntheses files once, instead of repetitively for each construct; and 2) am now triaging primer or assembly junction mispriming Tm calculation with the internal Bioperl Tm calculation function, and am only using Primer3 to re-calculate Tms for those with a bioperl Tm above the threshold. In terms of bug fixes: 1) fixed a bug in which during the template combinatorial design process, some temporary sequence files were getting generated as protein sequences instead of DNA sequences; and 2) fixed a bug that was improperly setting 5' or 3' extra CPEC bps for overconstrained junctions.
Version 3.2.0 (13-Jul-18)
Minor updates for two bug fixes and a minor new feature addition. Bug fixes: 1) when condensing assembly files, previously had not been outputting rows in the "Suggested Assembly Piece Contigs For Hierarchical Assembly" section for SLIC/Gibson/CPEC assemblies that have only one designed contig but whose "Likely Fail Flag" column should be still be "WARNING" -- fixed this so now these rows with single contains but with warnings are output; 2) in some SLIC/Gibson/CPEC assemblies with incompatibilities, attempting to design a hierarchical design process to resolve the incompatibilities resulted in an infinite loop -- fixed this to properly give up on designing the hierarchical design process. New feature: added, in both single construct and in condensed / combinatorial j5 output assembly files, an additional column to the Oligo Synthesis table containing the 3' sequences (annealing portions) of the oligos, which can be useful for re-computing the Tms of the annealing portions of the oligos with alternative Tm computing tools outside of j5 (i.e., other than with Primer3).
Version 3.1.2 (24-Jan-18)
Minor update pre-empting warning messages if master plasmids/oligos/direct syntheses files contain name matches that lack trailing number e.g. pVec instead of pVec00001.
Version 3.1.1 (25-Oct-17)
Minor bug fix for a sequence object mysteriously converting from a DNA alphabet to a protein alphabet.
Version 3.1.0 (18-Aug-17)
Added feature that adds Digest Linearized Pieces table to j5 assembly file output. Fixes bugs in the generation of combinatorial/condensed j5 assembly files in which Digest Linearized assembly piece Type ID numbering was incorrect, as well in these same files for missing Bin headers in the combinations of assembly pieces section when condensing combinatorial/condensed j5 assembly files.
Version 3.0.9 (27-May-17)
Added feature that enables list (one construct per row) combinatorial design layout types. Adds new j5 parameter COMBINATORIAL_DESIGN_LAYOUT_TYPE.
Version 3.0.8 (2-May-17)
Bug fix for issue resulting in j5 not properly checking if an assembled DNA product contains homologous sequence repeats.
Version 3.0.7 (17-March-17)
Minor bug fix for j5/BioPerl incorrectly assuming an ambiguous DNA encoding implied a protein alphabet.
Version 3.0.6 (14-March-17)
Minor bug fix for odd-numbered Golden-Gate overhang length (e.g., SapI has 3 bp overhangs) designs when relative overhang positions are shifted far away from neutral.
Version 3.0.5 (13-February-17)
Minor bug fix for routine attempting to annotate oligo binding sites on assembled DNA products, when there are no oligos to annotate.
Version 3.0.4 (12-January-17)
Change in use of from perl module Text::CSV_XS to Text::CSV_PP. Should not impact users, but enables j5 deployment on recent web servers that were having issues with Text::CSV_XS.
Version 3.0.3 (20-December-16)
Fixes for bugs affecting primer feature annotations and entire sequence-spanning feature annotations in j5 assembled construct Genbank format sequence file outputs.
Version 3.0.2 (8-December-16)
Minor fix for a bug affecting Primer3 design that incorrectly allowed the optimal primer size to be greater than the maximum primer size in certain situations.
Version 3.0.1 (5-December-16)
Minor fix for a bug affecting the merging of more than two contiguous sequence features when one of them spans the origin of a circular sequence.
Version 3.0.0 (28-November-16)
Minor bug fix for downstream automation distribute PCR reactions that prevented the condensed j5 assembly file from being input correctly.
Version 2.9.9 (9-November-16)
Minor change enabling functionality for the tracking/lineage of underlying parts in assembled constructs as sequence features.
Version 2.9.8 (14-October-16)
Enables back-to-back parts with DIGEST strategies. Has not been implemented yet for SLIC/Gibson/CPEC style assembly design, and if back-to-back DIGEST strategies are encountered during a mock assembly process, assumes a Golden Gate style assembly.
Version 2.9.7 (14-October-16)
Changes made to enable multiple DIGEST strategies in the same design, as long as the two DIGESTed parts are not back-to-back.
Version 2.9.6 (12-October-16)
Bug fixes for auto-annotation of FASTA format source sequences with part names rather than source sequence names, and for incorrectly computing full length oligo Tms.
Version 2.9.5 (16-September-16)
Added additional parameter to downstream automation parameters, namely THERMOCYCLERTYPE, which can currently either be set to "VERITI" (default) or "CFX384". No j5 behavior is changed with the default VERITI setting. If the parameter is set to CFX384, however, the way that j5 will arrange PCR reactions across a thermocycler block will be affected. Whereas with a Veriti thermocycler, annealing temperature zones are arranged from left to right, with the coolest zone at left and hottest at right; for a CFX384 thermocycler, annealing temperature zones are arranged top to bottom with the coolest zone at bottom and the hottest at top.
Version 2.9.4 (08-September-16)
Bug fix for incorrectly not applying/verifying Eugene rules for single construct designs.
Version 2.9.3 (29-August-16)
Bug fix for incorrectly issued j5 primer design mispriming warning messages that resulted for reverse primers targeting the 3' terminus of a linear template.
Version 2.9.2 (03-August-16)
Minor bug fix for assembled DNA construct feature merging issue resulting from GenBank feature annotations having lacking both /label="" and /gene="" tags.
Version 2.9.1 (28-June-16)
Minor bug fix for issue resulting from GenBank feature annotations having asterisk(s) ("*") in their labels.
Version 2.9.0 (28-June-16)
Minor bug fix for issue resulting from changes made in v2.8.7 for linear designs.
Version 2.8.9 (24-June-16)
Added a new j5 input parameter ("GOLDENGATETERMINIEXTRASEQDNASYNTHESISALT") to enable the specification of a sequence flanking the golden gate recognition site at the 3' end of a DNA synthesis assembly piece that is distinct from the sequence flanking the golden gate site at its 5' end (specified by "GOLDENGATETERMINIEXTRASEQ"). Certain DNA synthesis vendors do not allow inverted repeats at the termini of DNA synthesis fragments, so setting this new parameter (differently than the existing one) enables the user to specify different flanking sequences at the 5' and 3' ends of the synthetic fragment designs so as to not result in the terminal inverted repeat. This does not affect PCR-derived (other than synthetic DNA templates) assembly pieces, which will retain the inverted repeat at their termini and only be affected by the "GOLDENGATETERMINIEXTRASEQ" parameter.
Version 2.8.8 (24-June-16)
Minor bug fix for incorrect output plasmid rotation when primer annotations are not suppressed. Also, for output circular GenBank-format sequence files, feature annotations that have been broken at the origin are now being merged.
Version 2.8.7 (24-June-16)
Minor bug fix ensuring that the input forced 5' extra CPEC bps settings are applied to the correct assembly junction. Also a bug fix for the j5 output file Assembly Pieces section for SLIC/Gibson/CPEC style assembly, making sure that the forced or designed 5' extra CPEC bps are being output for the correct assembly junction.
Version 2.8.6 (24-May-16)
Change to Automation.pm that enables larger or smaller thermocycler blocks than multi-well plate definitions. For example, enables the use of 96-well thermocyclers when multi-well plate spec is 384-well. Assumes 3x2 column by row geometry. Should be further improved to support multiple multi-well plate specs and plate type assignments in code, but for now this works.
Version 2.8.5 (16-MAY-16)
Minor change ensuring that the optimal primer length sent to Primer3 does not exceed the maximum primer length.
Version 2.8.4 (03-SEP-15)
Modification of the mock assembly design process to exclude checking for sequence repeats within the assembled constructs. For some large constructs, the check for sequence repeats was significantly slowing down the mock assembly design process to an unacceptable extent on some systems. The check for sequence repeats within assembled constructs is still pursued for non-mock assembly design processes.
Version 2.8.3 (14-APR-15)
Minor fix for bug in distribute PCR reactions functionality that incorrectly resulted in not generating PR-PR output when only 7 (rather than 8 or more) source plates (including the PCR_mix_tubes plate) were specified.
Version 2.8.2 (10-MAR-15)
Minor fix for bug that incorrectly set 5' and 3' extra CPEC bps given 5' and 3' internal preferred overhangs/overlaps when a part was set in the reverse orientation.
Version 2.8.1 (07-JAN-15)
Minor bug fix needed to prevent endlessly processing a Genbank file containing a feature whose start position exceeds the length of the sequence.
Version 2.8.0 (09-JUL-14)
Minor bug fix needed to prevent the same overhang/overlap from being added more than once to a part's list of internal preferred overhang/overlaps.
Version 2.7.3 (13-May-14)
Important bug fix for assemblies whose first target part is derived from a non-GenBank source file.
Version 2.7.2 (12-May-14)
Implementation of outputting ACCESSION and VERSION numbers in j5 output GenBank format files.
Version 2.7.1 (05-May-14)
Minor change affecting the prioritization of putative overhang/overlap locations. When determining the overhang/overlap location for a given assembly junction, the order of prioritized objectives is now: 1) achieve full combinatorial re-use if possible; 2) if not possible to achieve full combinatorial re-use, then attempt to go with the preferred internal overhang/overlap positions (if any) for each part; 3) in the absence of preferred internal overhang/overlap positions, then attempt to go with the 5' and/or 3' preferred internal overhang/overlap positions for other parts in the same combinatorial bin that have identical 5' and/or 3' regions (respectively) as the current part; and 4) otherwise, if the assembly junction has a DNA synthesis or annealed oligo followed by a non-synthesis or annealed oligo (or vice versa), then place the overlap/overhang within the non-synthesis/annealed oligo piece where possible. The consequence of this last (fourth) objective is that flanking homology sequence to be appended to the 5' ends PCR primers will be minimized.
Version 2.7.0 (30-Apr-14)
New functionality within j5 to design the distribution of split and pool PCR reactions. Bug fixes for when determining embed in primer assembly strategies, particularly when the target construct is linear. New functionality within j5 to optionally append a UUID (universally unique identifier) to plasmid, oligo, and direct synthesis names.
Version 2.5.8 (18-MAR-14)
Minor bug fix for linear designs when designing a SLIC/Gibson/CPEC style assembly with the minimum overlap length greater than the Primer3 maximum of 36 bp.
Version 2.5.7 (10-FEB-14)
Minor bug fix during the automatic placement of overhangs/overlaps entirely within either the parts 5' or 3' to an overconstrained assembly junction when the parts 5' or 3' to the junction are either shorter than the minimal overhang/overlap length or contain degenerate bps which make them effectively shorter than the minimal overhang/overlap length. Made the automatic assembly strategy assignment to embed a short part in a primer more conservative, so that it is less likely post primer and overhang/overlap optimization that the optimized oligo will exceed the user-specified maximum oligo length.
Version 2.5.6 (08-FEB-14)
Completed implementation for optimal combinatorial part re-use in circumstances when full combinatorial part re-use is not possible because of insufficient sequence identity across all combinations at one or more assembly junctions. In these circumstances, overhangs/overlaps will be placed entirely either in the parts 5' or 3' to the over constrained assembly junction (i.e., not spanning the junction), depending on which side of the junction is anticipated to have fewer distinct overhangs/overlaps, so as to maximize assembly fragment reuse despite the overconstraint. Where possible, overhangs and overlaps are selected from regions of sequence identity between subsets of parts.
Version 2.5.5 (01-FEB-14)
Minor change that results in annotating primer binding sites only when the region to be annotated has a Tm above 5 degrees below the minimum specified primer Tm. Minor bug fix for Combinatorial Golden Gate assembly design when an overhang resulting from a digested template part is incompatible with an internal overhang found within a template part. For combinatorial assembly design when an assembly junction is overconstrained (sequence identity across all combinations at the junction is insufficient to identify an overhang/overlap that can be re-used across all combinations), a forced relative overhang/overlap inequality is now set to force all overhangs/overlaps to be either in the parts 5' or 3' to the junction, depending on which side of the junction is anticipated to have fewer distinct overhangs/overlaps so as to maximize assembly fragment reuse despite the overconstraint.
Version 2.5.4 (15-JAN-14)
Minor change that results in no longer annotating primer binding sites when the region to be annotated has a Tm below the minimum specified primer Tm. Initial implementation of secondary preferred 5' and 3' internal overhangs/overlaps for parts completed.
Version 2.5.3 (05-JAN-14)
Initial implementation of preferred 5' and 3' internal overhangs/overlaps for parts completed. Initial implementation of forced relative overhang/overlap regions completed.
Version 2.5.2 (04-JAN-14)
Minor bug fix for combinatorial SLIC/Gibson/CPEC when setting forced 5' and 3' extra flanking base pairs when some but not all of the assembly junctions are over-constrained. Initial progress towards enabling the user to set, and j5 to leverage, preferred 5' and 3' internal overhangs/overlaps for parts.
Version 2.5.1 (20-DEC-13)
Minor bug fix for situation occurring when attempting to re-use a non-identical oligo from the master library collection when the putative surrogate oligo is longer than the freshly designed oligo, and the designed oligo has no flanking 5' sequence.
Version 2.5.0 (19-DEC-13)
Minor bug fix for situation occurring when attempting to re-use a non-identical oligo from the master library collection when the putative surrogate oligo is much shorter than the freshly designed oligo. When a j5 design-specific error occurs, the latest version of the user's master lists plasmids, oligos, and DNA syntheses, and the last set of j5 parameters used, are no longer updated.
Version 2.4.9 (18-DEC-13)
Minor bug fixes. Fixed bug if master oligos or master DNA synthesis list files contained rows with names but without sequences. Fixed bug resulting from if an otherwise suitable DNA oligo substitute was rejected for length or Tm design constraints. Fixed bug that miscalculated the locations of assembly piece incompatibility hit locations.
Version 2.4.8 (16-DEC-13)
Change to j5 XML-RPC web services. In the event that there is a j5 design-specific error (as opposed to file system errors, for example), j5 will bundle up the working directory for the design process and return the results. This is useful for debugging purposes. For more information, see the j5 XML-RPC web services provider description page.
Version 2.4.7 (16-DEC-13)
To make forced relative overhang/overlap (FRO) position specification more consistent and intuitive, only FROs specified for target bins/target parts occurring at the 3' ends of assembly pieces will now impact the assembly design process (setting the relative overhang/overlap positions of the assembly junction to the 3' of the target bin/target part). This change will not affect many users, but will affect power-users and legacy designs that leverage j5 FRO functionality. This presents no change for assembly pieces derived from digests, DNA synthesis, or annealed oligos, but does present a change for assembly pieces derived from PCR reactions. Now, for PCR reactions, the FRO set for the 3'-most embed_in_reverse_primer target bin/target part will impact the assembly design. If there is no embed_in_reverse_primer target bin/target part, then, as before, the FRO set for the core target bin/target part of the PCR reaction (i.e., the template) will impact the assembly design.
Version 2.4.6 (15-DEC-13)
Minor bug fix for j5.pm concerning calculating the Tms of primers shorter than 3 bp. Also, embed in primer strategies no longer can extend the same primer through a DNA synthesis firewall. DNA synthesis firewalls now effectively mark assembly junctions, as no assembly piece can contain target parts on both sides of a firewall.
Version 2.4.5 (26-NOV-13)
Minor bug fix for j5.pm that affected importing j5 parameters for the golden gate recognition sequence and the golden gate termini extra sequence when the imported parameters contained white space characters.
Version 2.4.4 (25-NOV-13)
Added a feature that allows the flanking homology overlap length to be specified longer than the Primer3 maximum primer size (36 bp). This is important for users who demand very long overlaps (e.g. 50-100bp). When the overlap length is specified to be longer than 36 bp, the overlaps are not further optimized by Primer3 for Tm, GC clamp, etc.
Version 2.4.3 (24-NOV-13)
Added a feature that by default annotates the assembled output sequence(s) with the sites that the designed oligos bind to. There is a "SUPPRESS_PRIMER_ANNOTATIONS" parameter in the j5 parameters file that disables this feature. Added a feature that re-uses non-identical oligos from the master library collection when they will result in identical PCR products and they meet Tm and length thresholds. Fixed three bugs: 1) resulting when the minimum pcr size is very small and a part is smaller than the minimum primer length; 2) resulting when a part with a forward embed in primer strategy is followed by a reverse embed in primer strategy without an intervening PCR part; and 3) incorrectly enabled an embed in primer forced strategy for parts that are big enough to pcr amplify that are also too long to embed in primers.
Version 2.3.6 (04-NOV-13)
Bug fixes for parsing SBOL XML/RDF files that contain SequenceAnnotations on the negative strand.
Version 2.3.5 (02-NOV-13)
When an embed in primer strategy has been forced for a given part, j5 will now stick to this forced strategy even if the part is large enough to be PCR amplified.
Version 2.2.5 (01-OCT-13)
Minor bug fix for errors resulting from BLASTing against long sequences.
Version 2.0.6 (23-JUL-13)
Minor bug fix for how the default pure primer length is initialized.
Version 2.0.5 (17-JUL-13)
Minor change to j5 working directory structure and output file naming convention (appending four characters to the time stamp to guarantee uniqueness). This enables multiple j5 runs to be submitted within the same second, and also enables a single user to submit many runs without file system limitations becoming an issue. For the most part, most users will not observe any significant differences.
Version 2.0.0 (03-JUL-13)
Minor bug fix for relieving Primer3 constraints for extremely high Tms.
Version 1.9.3beta (30-MAY-13)
Minor bug fix for errors resulting from BLASTing against long sequences.
Version 1.9.2beta (29-MAY-13)
Minor bug fix for relieving Primer3 constraints for extremely stable hairpins.
Version 1.9.1beta (14-MAY-13)
Very minor change for bug affecting the splitting of origin-spanning sequence features at the origin, and making sure to split origin spanning features before converting a GenBank file to SBOL XML/RDF.
Version 1.9.0beta (06-MAY-13)
Minor fix for a bug when checking for repeated sequences within large (>25kb) assembly products. Optimal primer lengths are now set to the minimum primer length. Optimal primer Tms are now set to the maximum primer Tms. Optimal flanking homology sequence (Gibson overlap) Tms are now set to the maximum homology sequence (Gibson overlap) Tms. The GenBank <-> SBOL XML conversion process has been modified to ensure the uniqueness of SBOL displayIds within the server namespace (see Conversion of SBOL XML <-> GenBank sequence files for more information). Poly-X Primer3 design constraints are now relaxed prior to thermodynamic hairpin calculation constraints.
Version 1.8.0beta (02-APR-13)
Fix for bugs concerning user-specified 5' or 3' extra CPEC overlap bps that result in forced overlap sequences that are either shorter than the minimum allowable overlap length, or extend beyond the allowable region from which to select the overlap sequence (j5 now issues an error message and aborts the design process when this happens). Minor fix for a bug resulting from user-specified negative 5' extra CPEC overlap bps. Updated user manual to fix previously inaccurate depiction of how 5' or 3' extra CPEC overlap bps settings affect overlap sequence selection.
Version 1.6.1beta (12-FEB-13)
Minor fix for a bug (that resulted from changes made in version v1.6.0beta) that issued spurious SLIC/Gibson/CPEC assembly piece incompatibility warning messages.
Version 1.6.0beta (04-FEB-13)
New feature implemented that outputs warning messages when homologous sequence repeats are identified in DNA assembly products. Criteria (minimum sequence length, and maximum fraction of mismatches) for determining significant homologous sequence repeats are configurable within the set of j5 parameters. Note: warning messages are output only into individual construct j5 output files, and are not output into the combinatorial/condensed j5 output files.
Version 1.4.2beta (19-DEC-12)
Initial release of a multi-threaded version of j5. Limited performance improvements.
Version 1.4.1beta (12-Dec-12)
Minor bug fix for when a PCR forced assembly strategy is set for really small parts (e.g. only 5 bp) that really should be embedded in primers rather than directly amplified.
Version 1.4.0beta (08-Dec-12)
Minor bug fix when importing jbei-seq sequence files that contain single bp sequence features. For consistency, all sequence Tms are now calculated with Primer3 (if the sequence is longer than the 36 bp Primer3 maximum, only the 3' end of the sequence is used in the calculation, and for SLIC/Gibson/CPEC/SliCE assembly junctions, a warning message is issued that contains the BioPerl predicted Tm). Warning messages are now issued for DNA oligos that contain 5 or more Gs in a row (i.e., poly-G stretches), which could complicate DNA oligo synthesis.
Version 1.3.2beta (16-Nov-12)
Minor bug fix when importing jbei-seq sequence files that contain sequence features that span the origin.
Version 1.3.1beta (05-Nov-12)
Minor change coincident with the robot programming language name change from "PaR-PaR" to "PR-PR", which is not associated with PaR Systems, Inc. which claims ownership of the "PaR" mark.
Version 1.3.0beta (02-Nov-12)
Minor bug fix to assembly product sequence output.
Version 1.2.5beta (24-Sept-12)
Modest performance improvements.
Version 1.2.4beta (19-Sept-12)
Minor fixes for bugs when long DNA fragments/assembly pieces are BLAST'd for mispriming/incompatibility events. Minor bug fix for bug when no compatible set of Golden Gate assembly overhangs is identified.
Version 1.2.3beta (14-Sept-12)
Minor fixes for bugs when the first (5' most) or last (3' most) part in the target part order has a forced annealed oligo assembly strategy when the assembly product type is linear.
Version 1.2.0beta (7-Sept-12)
Minor fixes for bugs when parsing target part order list files with bins that contain no parts, and annotated GenBank files with single bp features on the complement strand.
Version 1.1.7beta (5-July-12)
Implementation of new PR-PR format output.
Version 1.1.5beta (18-June-12)
Implementation of SBOL XML format input and output. Addition of j5 SBOL XML <-> GenBank conversion utility, including XML-RPC method.
Version 1.1.3beta (8-June-12)
During the combinatorial SLIC/Gibson/CPEC or Golden Gate assembly design process, j5 no longer exits with an error message if a given assembly junction is over-constrained (i.e., it is not possible to design an assembly with full assembly piece re-use across all combinations). Instead, j5 now issues a warning message and relaxes the constraint that the overhang/overlap for the affected assembly junction(s) must be the same across all combinations. This allows j5 to complete the assembly design process, although the resulting assembly process cost will be greater than if full assembly piece re-use across all combinations had been achieved.
Version 1.1beta (28-May-12)
SLIC/Gibson/CPEC mispriming warning messages now output the DNA sub-sequences in addition to their bp locations within the incompatible assembly pieces. During the overhang selection process for Golden Gate-style assembly design, overhang sequences that are incompatible with overhangs (if any) resulting from the cleavage of internal type IIs restriction sites are now avoided.
Version 1.0beta (15-May-12)
Implementation of annealed oligos assembly strategies. Joined sequence features in jbei-seq XML format files are now split into separate feature entries to comply with BioPerl limitations. Minor bug fixes when parsing Genbank feature annotations. For the j5 simplified web interface, by default, all "Re-use last updated" checkboxes are unchecked.
Version 0.9alpha (24-APR-12)
Implementation of (combinatorial) mock assembly design.
Version 0.8alpha (19-APR-12)
Implementation of additional Eugene design specification rules: "AFTER", "BEFORE", "THEN", "NEXTTO", and "MORETHAN", along with the "NOT" rule negation operator. "NOTWITH" and "NOTMORETHAN" are still supported, although they may be deprecated going forward (The "NOT" negation operator in combination with "WITH" or "MORETHAN" is now preferred.) The meaning of the "WITH" operator has become more strict, and its previous definition is equivalent to the new "THEN" operator.
Version 0.7alpha (12-MAR-12)
Update of j5 for compatibility with Primer3 v2.3.1 and BLAST v2.2.26+. Minor changes to SLIC/Gibson/CPEC assembly piece output formatting.
Version 0.6alpha (07-FEB-12)
Implementation of linear DNA construct assembly design. By default, j5 now suppresses "pure" primer and "pure" PCR reaction output.
Version 0.5alpha (01-FEB-12)
Implementation of PR-PR configuration file output for automating the setup of PCR reactions with liquid handling robotics. Modifications made to decouple primer design Tm optima from flanking overlap sequence Tm optima, enabling shorter overlap lengths. Annotation of the entirety of each input FASTA-format sequence with a "misc_feature" labelled by the display ID of the FASTA file. j5 parameters now provide access to additional primer and flanking overlap sequence design constraints relating to complementarity.
Version 0.4alpha (19-DEC-11)
Combinatorial SLIC/Gibson/CPEC design has now been implemented. Minor changes to Target Part Order List File input and SLIC/Gibson/CPEC assembly piece output formatting.
Version 0.3alpha (24-NOV-11)
Minor change in the rank ordering of Primer3 violated design constraints to relieve.
Version 0.2alpha (02-JUN-11)
Initial change log reporting coinciding with release of j5.jbei.org public web server.