Changelog


Algorithm

Date:

April 11, 2023

  • enhancement 6b9db Users can now specify any genomic coordinates in a transript as the edit site.

Date:

Feburary 7, 2023

  • bug fix 6e2e5 Fixed a bug that causes mutating the same codons for a second time when scanning and fixing emerging cutsites in payload-homology chimeric regions.

  • bug fix 82c61 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

  • enhancement 78fd0 Changed the order of recoding in gRNAs and emerging cutsites (in window scan) to: 3’UTR -> codons -> intron -> 5’UTR

Date:

Feburary 4, 2023

  • enhancement 7da6a Changed the order of recoding in gRNAs to: codons -> 3’UTR -> intron -> 5’UTR

Date:

Feburary 1, 2023

  • bug fix e20ed 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

  • enhancement bf85b 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

  • bug fix f87f4 Avoid re-mutating by keeping track of mutated bases.

  • bug fix f87f4 Fixed an interference with mutation caused by marking codon-padding sequence with lower-case.

  • enhancement f87f4 Scan and undo isolated mutation of “N” in “NGG”.

Date:

January 20, 2023

  • bug fix 94ea9 Codon mutation won’t happen in some gRNAs in recut mode.

  • enhancement c2e92 Changed strand names to match the naming convention.


Portal

Date:

April 15, 2023

  • enhancement 6b9db Changed the interface to accomodate the input of custom genomic coordinates as edit sites.

Date:

Feburary 16, 2023

  • bug fix 004c6 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

  • enhancement 49990 Added a link in the landing page to a Google form to get an invitation code.

Date:

Feburary 14, 2023

  • enhancement 49990 Complete the name change to “protoSpaceJAM”. And several small changes, e.g. ‘Launch’ -> ‘Jam it’. Fixed typos.

Date:

Feburary 9, 2023

  • enhancement dced1 Consolidated donor length parameters into one box, and donor recoding parameters into one box.

Date:

Feburary 1, 2023

  • enhancement b6b91 Change the default minumn homology arm length (dsDNA) to 200.

  • bug fix b6b91 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

  • enhancement f0ad7 Add a maximum limit of 384 entries per submission list.

Date:

January 26, 2023

  • enhancement 0c23a Default changed to “non-target strand” (including the example).

  • enhancement 54621 Default changed to “Prioritize recoding in PAM” (including the example).