Changelog

Algorithm

Date: June 05, 2024 Added payload protein translation to the donor genbank output file.
Date: May 29, 2024 Fixed a bug where different designs may have the same donor name.
Date: May 29, 2024 Added coding feature annotation to donor genbank output file.
Date: April 22, 2024 Users can now omit transcript IDs when specifying custom genomic coordinates. (recoding will not be aware of coding regions and splice junctions).
Date: April 21, 2024 gRNA weight are now raised to the power of the scaling factor.
Date: April 8, 2024 Added an argument to recode only in coding region.
Date: April 8, 2024 The scaling factor of gRNA scoring weights can be zero, the corresponding weight will be ignored if the scaling factor is zero.
Date: April 4, 2024 Fixed an issue preventing homology arm length be less than 200 bp in dsDNA donor mode.
Date: March 7, 2024 Add scaling factors for weights used in gRNA scoring/ranking.
Date: March 1, 2024 Add support for SpCas9-VQR and enAsCas12a.
Date: June 26, 2023 Use Bowtie as the default aligner to check unintended PCR products in primer design.
Date: June 2, 2023 Add an option to disable penalizing gRNAs that cut in UTRs or near splice junctions.
Date: June 2, 2023 Output both trimmed and untrimmed dsDNA donors in the results.
Date: June 2, 2023 Generate a unique name for each gRNA, donor, and trimmed donor.
Date: May 15, 2023 Results now include the strands of gene, gRNA and donor ( + denotes the forward strand and - denotes the reverse strands).
Date: April 11, 2023 Users can now specify any genomic coordinates in a transcript as the edit site.
Date: Feburary 7, 2023 Fixed a bug that causes mutating the same codons for a second time when scanning and fixing emerging cutsites in payload-homology chimeric regions.
Date: Feburary 7, 2023 Fixed a bug where the last one in an array of recoded nucleoties sometimes were not reflected in the final donor.
Date: Feburary 6, 2023 Changed the order of recoding in gRNAs and emerging cutsites (in window scan) to: 3’UTR -> codons -> intron -> 5’UTR.
Date: Feburary 4, 2023 Changed the order of recoding in gRNAs to: codons -> 3’UTR -> intron -> 5’UTR.
Date: Feburary 1, 2023 Fixed two bugs in the dsDNA trimming logic: 1) the right arm was not trimming correctly, 2) report synthesis problems remaining after the trimming step.
Date: January 25, 2023 Fine-tuned the off-limit range for recoding near junctions. Now avoiding 3bp/6bp from exon/intron side of the exon/intron junction, and 3bp/2bp from intron/exon side of the intron/exon junction.
Date: January 24, 2023 Avoid re-mutating by keeping track of mutated bases. Fixed an interference with mutation caused by marking codon-padding sequence with lower-case.
Date: January 24, 2023 Scan and undo isolated mutation of “N” in “NGG”.
Date: January 20, 2023 Codon mutation won’t happen in some gRNAs in recut mode.
Date: January 20, 2023 Changed strand names to match the naming convention.

Portal

Date: May 29, 2024 Added an interface label: “Looking for another PAM? Here are instructions to onboard your own. You can also contact us for help”
Date: May 29, 2024 change interface label: minimum HA length -> stop trimming if HA are shorter than (use 0 base-pairs to inactivate trimming).
Date: May 29, 2024 Added buttons “give us feed back / report a problem”.
Date: April 23, 2024 Fix error handling when tag and linker are both empty.
Date: April 23, 2024 Allow users to omit the transcript ID column entirely when specifying custom genomic coordinates.
Date: April 22, 2024 Added a warning message when genomic coordinates are used without specifying transcript IDs.
Date: April 22, 2024 Users can now omit transcript IDs when specifying custom genomic coordinates. (recoding will not be aware of coding regions and splice junctions).
Date: April 21, 2024 Added a warning message when the primer deisgn can’t utilize precomputed primers (longer wait times).
Date: April 21, 2024 Added a warning message when the PCR amplicon length is shorter than the DNA donor (PCR amplicon could be generated from the DNA donor).
Date: April 21, 2024 Added a warning message when the DNA donor length is shorter than the payload (there is no room for homology arms).
Date: April 16, 2024 Tunable primer parameters (e.g. amplicon size and Tm range).
Date: April 15, 2024 Improved santitization of user input.
Date: April 14, 2024 Annotated DNA donor in GenBank format.
Date: March 07, 2024 Added buttons to delete individual submissions from the submission list .
Date: March 07, 2024 Added an option to skip the linker sequence.
Date: March 07, 2024 User-tunable parameters will remain last used values when users switch between design steps.
Date: March 01, 2024 Fixed a bug where payloads are empty when defined by selecting tag and linker.
Date: March 01, 2024 Add a nuclease selection dropdown for SpCas9 and enAsCas12a.
Date: Janurary 06, 2024 Add tooltip instruction for terminus offset (e.g. enable insertions at n bp up and downstream of terminus).
Date: Janurary 06, 2024 Fixed a parsing issue preventing the use of submission lists csv file (downloaded from a job) in uploading and populating a new submission (this issue didn’t affect the example template).
Date: July 08, 2023 Fixed a bug causing editing payload sequence custom genomic coordinate to fail.
Date: July 08, 2023 Make automatic the default strand selection mode for ssODN donors.
Date: July 06, 2023 Implement a maximum wait time of 5min for each ad hoc GenoPrimer design.
Date: June 26, 2023 Add progress indicator for pJAM.
Date: June 26, 2023 Add gene ID and gene symbol for primer output.
Date: June 12, 2023 Add privacy and cookie policy.
Date: May 19, 2023 Updated to the CZ Biohub SF logo, improved helper text in several places.
Date: May 19, 2023 CSV upload is updated to work with the new columns in the submission list.
Date: May 15, 2023 Genotyping primers are fetched from precomputed results, and if not found, are designed on the fly.
Date: April 15, 2023 Changed the interface to accomodate the input of custom genomic coordinates as edit sites.
Date: Feburary 16, 2023 Entry number are now correct when there are 2+ gRNAs for each design. Associated change: ProtospaceJAM will read “Entry” from input, and if fails, uses an auto increment.
Date: Feburary 14, 2023 Added a link in the landing page to a Google form to get an invitation code. Complete the name change to “protoSpaceJAM”. And several small changes, e.g. ‘Launch’ -> ‘Jam it’. Fixed typos.
Date: Feburary 9, 2023 Consolidated donor length parameters into one box, and donor recoding parameters into one box.
Date: Feburary 1, 2023 Change the default minumn homology arm length (dsDNA) to 200.
Date: Feburary 1, 2023 Made “clear example” and “reset button” buttons work correctly, both will reset to the following defaults: Genome: Human, Genes: None, number of gRNA:1, DNA donor type: ssDNA, HA arm length to consider: 500, target strand: non-target strand, recode intensity:full, prioritize recoding in: PAM, minimum homology arm length: 200, enforce maximum donor length: 200, recut cfd threshold: 0.03.
Date: January 27, 2023 Add a maximum limit of 384 entries per submission list.
Date: January 26, 2023 Default changed to “non-target strand” (including the example).
Date: January 26, 2023 Default changed to “Prioritize recoding in PAM” (including the example).