News and updates
  • News and updates for CRISPRSuite programs and tools: CRISPRTarget, CRISPRDetect, CRISPRBank, CRISPRHost
CRISPRTarget is part of CRISPRSuite (more information)
CRISPRSuite
  • 18/1/2024 All RefSeq and Genbank phage updated.
  • 21/11/2023 All RefSeq and Genbank phage updated.
  • 21/8/2023 Genbank phage updated.
  • 29/7/2023 A prerelease version of commandline CRISPRTarget is available. Contact A/P Chris Brown if you wish to test it.
  • 29/7/2023 All RefSeq updated.
  • 11/6/2023 All RefSeq, and GenBank phage updated.
  • 16/3/2023 Current sizes of fasta files in bytes are: 2.1G plasmid, 4.1G archaea, 0.5M viral, 1.3G phage, 0.6G, Phast (3/2018), 1.6G islandviewer (11/2018), 78G IMGVR (10/2022), 21G HuVirDB (3/2019), 116G ENV. Databases that have no available updates last two months are listed with date of most recent release available.
  • 20/1/2023 All RefSeq  updated.
  • 31/12/2022 GenBank phage and ENV updated.
  • 20/11/2023 All RefSeq  updated.
  • 20/10/2022 GenBank phage updated according to NCBI's two month cycle.
  • 13/10/2022 IMGVR v4 Sept 2022 (or 6.1). IMG_VR_2022-09-20_6.1 - IMG/VR v4 - high-confidence genomes only (~80Gb) but 2x as large in size and 10 diversity as previous IMGR database from 2020. Previous version is available in as 'Test' on the database menu.
  • 20/92022 All RefSeq, and ENV (from Blast) updated according to NCBI's two month cycle
  • 27/8/2022 GenBank phage and ENV updated according to NCBI's two month cycle
  • 20/72022 All RefSeq, and ENV (from Blast) updated according to NCBI's two month cycle
  • 31/05/2022 GenBank phage and ENV updated according to NCBI's two month cycle. 
  • 31/05/2022 Genbank viral is no longer offered as it too big with COVID sequences. Use Refseq viral or phage or IMGVR
  •  24/03/2022 All RefSeq  updated according to NCBI's two month cycle.
  • 27/12/2022 All GenBank updated according to NCBI's two month cycle. 
  •  10/01/2022  All RefSeq, and ENV (from Blast) updated according to NCBI's two month cycle. NCBI Plasmid has 39,967 sequences.
  •  20/12/2021 All GenBank updated according to NCBI's two month cycle. GB Phage has 30,214 sequences.
  •  11/011/2021 All RefSeq, and ENV (from Blast) updated according to NCBI's two month cycle. Genbank Phage and RefSeq Plasmid updated to files timestamped 02/11/2021 from 15th Oct Genbank Release, 29814 sequences.    
  •  20/10/2021 All GenBank updated according to NCBI's two month cycle.     
  •  20/07/2021 All RefSeq and Genbank updated according to NCBI's two month cycle. PHAGE is now from Genbank Phage as done prior to 5/2021.    
  •  24/05/2021 All RefSeq updated according to NCBI's two month cycle.    
  • 24/05/2021 Genbank phage updated by Entrez serach  'phage[All Fields] AND (viruses[filter] AND biomol_genomic[PROP] AND ddbj_embl_genbank[filter])' 31517 accessions,  includes some non-phage containing sequences e.g. prophages within genomes. The last precompileded by NCBI gbphg.seq files were dated 16 2 2021 (22,260   accessions, CRISPRTarget  will return to Genbank Phage when it is updated .  Note: Entrez search phage[All Fields] AND (viruses[filter] AND biomol_genomic[PROP] AND ddbj_embl_genbank[filter]) NOT "Bacteria"[Organism] gives a more restricted dataset, that is slighly larger than Genbank phage.
  • 09/3/2021 All RefSeq updated according to NCBI's two month cycle (NCBI files dated 2021-03-05)
  • 24/2/2021 All Genbank updated according to NCBI's two month cycle (NCBI files dated 2021-02-16)
  • 21/2/2020. We have a commandline rewrite of CRISPRTarget in final development. Email chris.brown@otago.ac.nz if you would like to try it for your latest research. It has some options for increased speed and sensitvity.
  • 02/11/2020. The IMGVR database paper is out great work from the IMGVR team!
  • Oct 2020. We have been experiencing very high demand. Please email us if you have any problems or unexpected behaviours.
  • 1/11/2020 IMGVR update the version being used is the latest 43 Gb  2,377,994 sequences, 12 Oct 2020 v5.1 or 'IMG_VR_2020-10-12_5.1 - IMG/VR v3' This includes IMGVR viral contigs with IDs like IMGVR_UViG_2579779064_000006|2579779064|2579849396|1-17041, some genomes from RefSeq with IDs like NC_027986.1, and other entries Gammaproteobacteria_gi_553770258, and UGV-GENOME-3293712.
  • The previous IMGVR v2 version is provided as 'test'.
  • 21/10/2020 All Genbank updated accordig to NCBI's two month cycle 
  • 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 [returned to blastn 8/2020]  
  • 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. [Recreated from BLAST database file 7/11/2021 onwards] 
  • 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.
  • CRISPR, 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 it, keep it large e.g. 1e9  if you have a high E value e.g. 1

  • 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 , doi: 10.4161/rna.24046
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