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CRISPRHost help

This application takes a partial prokaryotic virus sequence and predicts the host. It utilizes the fact that foreign DNA molecules such as phage genomes, plasmid and mobile genetic elements, can be included as spacers in CRISPR arrays in bacteria and archaea. Therefore, spacers in CRISPR-arrays provide an indication of what hosts have defended against the virus, or a similar virus. FASTA-formatted BLAST databases of CRISPR spacers from bacteria and archaea (predicted by CRISPRDetect 2.4) were built. In the database, each spacer sequence was linked to the genomic and taxonomic information of source organisms in the headers. When DNA sequences are provided as queries by the user, BLASTN will be used to find any spacer targets in each sequence, and the genomic and taxonomical information of their owners can be obtained.

Validation data, and R scripts used for PPV calculations and testing statistics are in this GitHub repo: By considering spacer matches with an e-value no higher than 1e-8 and at least 95% of all nucleotides in spacer-target hybrids to be matched, the PPV calculations (by exact name-matching) are the following.

PPV-Order PPV-Family PPV-Genus
Bacteria 0.97 0.96 0.92
Archaea 0.98 0.98 0.7

A web version is available through a Galaxy interface here: (under "Virus: Classification").

The source directory was first uploaded to GitHub in 2018, and was presented by Chris Brown at CRISPR2019, Molecular Biology of Archaea 2019, and Asian Transcription Conference 2019.

A manuscript is in preparation (Chyou, Biswas, Fineran, Brown).

General usage

As a minimum, nucleic-acid sequences need to be provided as a FASTA or a multi-FASTA formatted file, along with the path to the output directory. Additional options (next section) can also be specified. CRISPRHost can be called outside the source directory.

perl -in <fasta_path> -out <dir_path> <options>
perl /path/ -in <fasta_path> -out <dir_path> <options>


The full list of command-line options is displayed below.

-in <path>                   [Required] A FASTA file of viral genome, mobile genetic elements, or sequences.
-out <path>                  [Required] Path to the output directory.
-kingdom <A|B|AB>            Select a kingdom (A=archaea, B=bacteria, AB=archaea+bacteria). 
                             The corresponding BLASTDB of CRISPR spacers (non-redundant) will then be used:
                                1. A: RefSeq95 archaeal, DB/CRISPRBankSpacers_4_95_2555_100_archaea_refseq_nr.fa
	                        2. B: RefSeq95 bacterial, DB/CRISPRBankSpacers_4_95_2555_100_bacteria_refseq_nr.fa
  	                        3. AB: RedSeq95 archaeal+bacterial, DB/CRISPRBankSpacers_4_95_2555_100_all_refseq_nr.fa
                             During the first run, the app will unzip "" for the DB directory.
                             Default: AB.
-mask_arrays                 Optionally run MINCED to predict predict arrays and mask them using BEDTOOLS.
-dbsize <integer>            Number of nucleotides in BLASTDB, optional parameter for BLASTN. Default: 10000.
-e_cutoff <numerical>        E-value cutoff for BLASTN spacer hits. Default: 0.001.
-b_cutoff <numerical>        Bit-score cutoff for BLASTN spacer hits. Default: 50.
-pr_cutoff <numerical 0-1>   Minimum proportion of base-paired nucleotides in spacer-target hybrids. Default: 0.7.
-min_nocsh <integer>         Minimum number of CRISPR spacer hits per sequence. Default: 1.
-max_target_seqs <integer>   Maximum number of hits to be returned by BLASTN for post-processing. Default: 500.
-h                           Show this help.
-help                        Show this help (same as -h).      

Output files

The following output files are generated.

summary.csv                Files showing the key results. The columns are:

                               1. Spacer hit statistics
                               VIRAL_GENOME                Viral genome identifier.
                               N_HOST_SPACER               Number of hits from spacers of the same sequence.
                               E_VALUE                     BLASTN e-value.
                               BITSCORE                    BLASTN bitscore.
                               PROP_NT_MATCHED_IN_HYBRID   Proportion of matched nucleotide in a spacer-target hybrid.
                               2. Attributes of matched spacers
                               SPACER_ID                   Spacer identifier.
                               KNOWN_SPECIES               A list of species where the same spacer can be found. 
                                                           These species are the predicted hosts.
                               TARGET_ALIGN_START          Start-coordinate of the target alignment.
                               SEQ_TARGET_ALIGNED          Sequence of the spacer target.
                               SPACER_ORI_ALIGN            Whether the match is corresponding to the reverse-complement 
                                                           of the spacer (minus) or not (plus). 
full_results.csv             Files showing the key results in summary.csv, with additional information and statistics
spacer_matched.fna           A list of spacers matched in multi-FASTA format.

c_arrays.gff                 Any CRISPR arrays found by MINCED and masked by BEDTOOLS, if -mask_arrays is used                         


CRISPRHost requires the following dependencies. The executables of applications are provided, but BioPerl, R and Rscript will need to be installed separately.

  1. NCBI BLAST suite: blastn, makeblastdb and blastdbcmd (provided)
  2. Bedtools (provided)
  3. minced (provided)
  4. Perl library BioPerl
  5. R 3.6+ (no add-on libraries needed) and Rscript


Example commands:

perl -in NC_034623.fna -out test_NC_034623
perl -in NC_034623.fna -out test_NC_034623 -kingdom AB
perl -in NC_034623.fna -out test_NC_034623 -kingdom AB -mask_arrays


Predict viral hosts by BLASTN sequence alignment using CRISPR spacers.






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