Latest updates:

  1. Dec 3 2018 - Updated CHO-K1 genome with an assembly with gene IDs (GCF_000223135.1/CriGri_1.0). Example gene ID: XM_007607631.2
  2. Dec 3 2018 - Simplified the Solanum lycopersicum (SL3.0) gene IDs by removing the period and subsequent number. E.g. Solyc03g115850.3 is now Solyc03g115850
  3. Aug 22 2018 - Fixed a bug where off-targets with 3 mismatches were not always found. CHOPCHOP is now able to find ALL off-targets with up to 3 mismatches, but we decided to use early stopping ('>=' sign indicates that there exist potentially even more mismatches than reported). Early stopping is only used when there is more than k (300 for CRISPR, 200 for TALEN) off-targets already found.

This is the second edition of CHOPCHOP. We have made the following updates.

CHOPCHOP has completely new features:

  1. CRISPR/Cpf1 mode
  2. CRISPR/Cas9 nickase mode
  3. targeting to promoter regions
  4. support for truncated sgRNAs
  5. offtarget search up to 3 missmatches
  6. self-complementarity scoring for sgRNAs
  7. support for orthologous type II CRISPR/Cas PAMs
  8. new efficiency scoring metrics based on large-scale studies
  9. scoring of complementarity of sgRNAs against backbone regions

In addition, the web interface has the following improvements:

  1. mobile friendly
  2. lots of new organisms
  3. cookies that remember your last query
  4. downloadable table with designed primers
  5. results integrated with the UCSC genome browser

CHOPCHOP has fixed the following bugs:

  1. fasta/genome input switch history
  2. fasta input scoring of off-targets
  3. fasta input bug
  4. repetitive sgRNAs
  5. shift in results view
  6. infrequent strand issue
  7. summary of off-targets at the PAM N position