Many thanks to the users that have contacted me, suggested features and tested them!

Sep 2022

On 17.09.2022, Jean-Stéphane Joly passed away after having battled his disease with enormous courage for half of his life. Jean-Stéphane jumpstarted CRISPOR with French ANR funding and his lab has been running the server since then. For it, he found a programmer and former PhD student, (Max Haeussler, now UCSC) and an outstanding biologist advisor (Jean-Paul Concordet, Paris Natural History Museum). His relentless energy, prolific ideas and constant passion was sometimes hard to channel, but always an inspiration driving many of his collaborators. Unsurprisingly, all of his students chose a career in science. Without Jean-Stéphane, a lot of other non-mainstream model organism infrastructure would not exist, e.g. Meganucleases for transgenesis. He also published on Zebrafish, Ciona and Medaka. We will continue to support and update Crispor to keep part of his legacy alive, but will never be able to match his energy and passion.
See also: Obituary (in French)

Version 5.01, Aug 2022 - small fix

  • Sometimes PAMs were misplaced on the sequence plot, HT to Kirsten Cunningham-Bowland, Johns Hopkins

    Version 5.00, Jan 2022 - small fixes

  • CasX target was on the wrong strand, Jason Fernandes, Scribetx Inc
  • On the sequence viewer, cleavage sites were shown at the wrong location when using Crispor on a new OSX with M1 CPU and Asian fonts, Taro Nakamura, Nat Inst Basic Biol Japan
  • Version 4.99, April 2021 - more enzymes

  • Added Inscripta MAD7 enzyme, C. Dustin Rubinstein, Univ of Wisconsin-Madison
  • adding Thermocas9, Panji Banurea, Bogor Agricultural University, Indonesia
  • adding SpRY, Ben Kleinstiver, Harvard
  • adding mutation overview for the last 3bp of the guide, Tom Schreiber, IPB Halle, Germany
  • Activated exon display, a lot of users have asked for this

    Version 4.98, June 2020 - small improvements

  • Better Geneious export, Brian Vogler, Bayer
  • Better Snapgene export, Yarin Aknin, Hebrew University
  • Fix saCas9 scaffold primers, Santiago Chávez, Udelar, Uruguay
  • Invisible work towords a future exon display, Max

    Version 4.97, Dec 2019 - small bugfixes

  • "Only exons" now works for tables with many off-targets, Thom Saunders, U Michigan
  • Off-target primers fixed, thanks Francois Hafezi, Univ Luxemburg and Zuzanna Bukowy, Polish Acad of Sciences and
  • Allowing 21bp guides for Cpf1, thanks Suzy Markossian, ENS Lyon, France
  • Fixing some repetitive guides not getting flagged as repetitive, big thanks to Josh Tycko

    Version 4.96, Oct 2019 - changes to Cpf1 search

  • Allowing TTTN as off-targets for Cpf1, removing Graf et al warnings for anything but NGG pams, thanks to Florian Hahn, Rothamsted Research, UK
  • Fixing layout of guide in the sequence view which lead to PAMs being not under their sequence, thanks Alessandro Bellan, Uni Padova, Italy

    Version 4.95, Sep 2019 - more output options, moving towards a better hg38 genome

  • Excel output now has Graf columns and the option of adding all scores, thanks to Peter Stepper, OAW Vienna
  • hg38 now defaults to the "analysis set" hopefully this will solve problems with _alts and the PAR region, thanks to Evgeni Frenkel, MIT
  • The command line version now accepts .bed input, thanks to Evgeni Frenkel, MIT

    Version 4.93, August 8 2019 - better cDNA detection

  • cDNA input is now better detected. Thanks to Imke De Grahl, Uni Hamburg

    Version 4.92, June 23 2019 - Bugfix for Cpf1

  • Fixed an old bug, which we had since CRISPOR 4. All PAMs that contain "V" were never found on the reverse strand. Thansk to Gemma Codner, MRC Harwell

    Version 4.91, May 1st 2019 - Lindel predictions, Graf et al criteria

    Version 4.8, Mar 2019 - Queueing changes, Off-target primers

    Version 4.7, Jan 2019 - PAR loci, CCtop

    Version 4.6, Nov 2018 - alternate loci

    Version 4.5, Sep 2018 - saCas9 specificity scores

    Version 4.4, May 2018 - Cpf1/saCas9 scores

    Version 4.3, Oct 2017 - CRISPOR Batch

    Version 4.2, June 2017 - Saturation mutagenesis

    Version 4.0, Mar 2017 - Cpf1, Variants, sequence names, AddGene plasmids, UCSC tracks

    The following features were implemented. Many thanks to the people that have contacted me, suggested features and tested them!