News and updates
  • News and updates for CRISPRSuite programs and tools: CRISPRTarget, CRISPRDetect, CRISPRBank, CRISPRHost ..
CRISPRTarget is part of CRISPRSuite (more information)
CRISPRSuite
  • 21/9/2020 All RefSeq   updated to 202 accordig to NCBI's two month cycle
  • 21/8/2020 All Genbank updated accordig to NCBI's two month cycle 
  • 25/6/2020 Trialling the use of vsearch rather than blastn to increase sensitivity
  • 25/6/2020 Typing using CRISPRVasTyper on repeats
  • 1/6/2020 RefSeq and Genbank update. Note the ENV database can no longer be updated as NCBI have stopped providing it in a suitable form. It will remain at the version of 2/2020 until further notice.
  • 21/2/2020 Genbank virus and phage update
  • 11/1/2020 Refseq update 98, CRISPRBank precomputed arrays are from RefSeq95 (7/2019)
  • 15/12/2019 Genbank virus added. RefSeq bacteria removed as it was impractical to search this large redundant database (~700 Gb) and of limited biological relevance. Users could use blastn or STSS as alternatives depending on the question being addressed. Genbank updates including ENV.
  • 26/9/2019 RefSeq update
  • 25/8/2019 Genbank update
  • 28/6/2019 RefSeq update
  • 14/6/2019-16/6/2019   Output now links nicely to IMGVR.
  • 25/5/2019 Moved to new server, added databases IMGVR, HumVirDB, PHAST (redundancy and human chromosomes removed)
  • 21/5/2019 RefSeq update, ENV update
  • 23/4/2019 Genbank phage and Genbank viral updated
  • 22/3/2019 RefSeq update
  • 22/2/2019 Genbank phage and Genbank viral updated
  • 16/1/2019 RefSeq Databases now updated to RefSeq 92 (Jan 2019) as per the regular cycle. 'Blast' databaes also updated (env_nt, nt)
  • IMGVR added 8/2018 version see help for more information
  • 2/8/2018 tracrRNAfinder published and availble through Galaxy. Chyou et al 2018 https://www.ncbi.nlm.nih.gov/pubmed/29995560
  • onlymajor changes listed (not routine updates) listed here pre 2019
  • Databases will be updated after each release of Genbank (even months) or RefSeq (odd months). The nt and env databases come from the BLAST databases and will be updated monthly.
  • In future there will be an automatic update on the 21st of each month or when the database is released, and only the current version listed.
  • 31/10/2017 Genbank release updated phage, env (Blast)
  • 29/11/2016 Update env, removed access to NT as there is little reason to search this (mainly eukaryotic genomes). If this is a problem please request access (chris.brown otago.ac.nz)
  • 12/8/2016 CRISPRDetect v 2.2 released. Faster on fasta files!
  • 25/5/2016 CRISPRDetect published in BMC Genomics
  • 27/2/2016 CRISPRDetect v 2.1 released.
  • Final version of CRISPRDetect completed. v2.0 and on the web and command line. All earlier '1' versions were testing versions and should be updated to the release version as there may be minor bugs.

  • Guide to using CRISPRTarget published:
    Computational Detection of CRISPR/crRNA Targets.
    Ambarish Biswas, Peter C Fineran, Chris M Brown
    The CRISPR-Cas systems in bacteria and archaea provide protection by targeting foreign nucleic acids. The sequence of the "spacers" within CRISPR arrays specifically determines the targets in invader genomes. These spacers provide the short specific RNA nucleotide sequences within the guide crRNAs. In addition to complementarity in the spacer-target (protospacer) interaction, short flanking protospacer adjacent motifs (PAMs), or mismatching flanks have a discriminatory role in accurate target detection. Here, we describe a bioinformatic method, called CRISPRTarget, to use the sequence of a CRISPR array (e.g., predicted via CRISPRDetect/CRISPRDirection) to identify the foreign nucleic acids it targets.
    Methods in molecular biology (Clifton, N.J.) 01/2015; 1311:77-89. DOI:10.1007/978-1-4939-2687-9_5
    http://link.springer.com/protocol/10.1007%2F978-1-4939-2687-9_5
  • ACLAME and the CAMERA sets used here have not changed so will not be updated unless they do.
  • All databases are being updated to the latest version completed 13/5/2015. As RefSeq have split the previous Microbial database into two Archaea and Bacteria we have also done this. Databases will be updated after each release of Genbank (even months) or RefSeq (odd months). The nt and env databases come from the BLAST databases and will be updated monthly.

  • Added database size parameter for blast on 22/02/2013.

  • If you use CRISPRTarget please cite:
    Biswas, A., Gagnon, J.N., Brouns, S.J., Fineran, P.C., and Brown, C.M. (2013) CRISPRTarget: Bioinformatic prediction and analysis of crRNA targets. RNA Biol 10 (5): 817–827. Free fulltext