Welcome to CRISPRome

spacer_fasta.tar.gz

The three files in the spacer_fasta directory contain unique spacer sequences after deduplication within each CRISPR array:

• archaea_unique_spacer.fa: Unique spacer sequences from archaea.
  
• bacteria_unique_spacer.fa: Unique spacer sequences from bacteria.
  
• environment_unique_spacer.fa: Unique spacer sequences from environmental samples.

crispr_cas_info.tar.gz

The crispr_cas_info directory contains CRISPR-Cas information from archaea, bacteria, and six environmental microbial samples, including locus details, subtype classification, repeat sequences, and statistical summaries.

source_target_network.tar.gz

The source_target_network directory contains archaeal and bacterial CRISPR source-target network data.

The file archaea_bacteria_net_info.tsv represents CRISPR source-target network pairs with the following columns:

• genome_id – Identifier for the source genome.
  
• total_array – Total number of CRISPR arrays in the genome.
  
• total_spacer – Total number of spacers in the genome.
  
• unique_spacer_count – Number of unique spacers after deduplication.
  
• array_id – Identifier for the specific CRISPR array.
  
• spacer_id – Identifier for the specific spacer.
  
• source_domain – Domain classification of the source organism (e.g., Archaea or Bacteria).
  
• source_name – Scientific name of the source organism.
  
• source_taxid – NCBI Taxonomy ID of the source organism.
  
• source_lineage – Taxonomic lineage of the source organism.
  
• target_domain – Domain classification of the target entity.
  
• target_name – Scientific name of the target entity.
  
• target_taxid – NCBI Taxonomy ID of the target entity.
  
• target_lineage – Taxonomic lineage of the target entity.

spacer_fasta.tar.gz

The source_target_loci_info directory contains the following files:

archaea_spacer_mapping_results bacteria_spacer_mapping_results environment_spacer_mapping_results These files contain spacer mapping results with the following columns:

• unique_spacer_id – Identifier for the unique spacer in the analysis.
• target_taxid – NCBI Taxonomy ID of the target organism, identifying the species involved in the target region.
• target_lineage – Taxonomic lineage of the target organism, providing its hierarchical classification.
• target_kingdom – Kingdom classification of the target organism (e.g., Bacteria, Archaea).
• sseqid – Sequence identifier for the subject sequence (target genome) in the BLAST alignment.
• pident – Percentage of identical matches between the spacer (query) and the subject sequence (target genome) in the alignment.
• length – Length of the aligned region between the spacer and the subject sequence in the BLAST result.
• mismatch – Number of mismatches (non-identical bases) between the spacer and the subject sequence in the alignment.
• gapopen – Number of gap openings (insertions or deletions) introduced in the alignment.
• qstart – Start position of the spacer sequence (query) in the alignment.
• qend – End position of the spacer sequence (query) in the alignment.
• start – Start position of the subject sequence (target genome) in the alignment.
• send – End position of the subject sequence (target genome) in the alignment.
• evalue – Expectation value of the alignment, representing how likely the alignment is to occur by chance.
• bitscore – Score of the alignment in bits, indicating the strength of the match; higher bitscores represent better alignment quality.
• database – The database used for the BLAST alignment, which could be a genomic database or other sequence repository.
• sseqid_corrected – Corrected version of the sequence identifier for the subject sequence.
• sbjct_taxid (before LCA) – NCBI Taxonomy ID of the subject sequence before the Lowest Common Ancestor (LCA) analysis was performed.
• target_genome – Identifier for the target genome, representing the organism whose genome is being analyzed.
• loci_start (gene annotation) – Start position of the gene annotation in the target loci within the target genome, marking the beginning of the annotated gene region.
• loci_end (gene annotation) – End position of the gene annotation in the target loci within the target genome, marking the conclusion of the annotated gene region.
• gene_or_not – Indicates whether the locus corresponds to a gene or a non-coding region (e.g., “gene” for coding regions, “intergene” for intergenic or non-coding regions).
• sseq_length – Length of the subject sequence involved in the BLAST alignment with the spacer.
• relative_loci – Position of the loci in the context of the gene/intergene, indicating where the alignment region appears relative to the entire gene/intergene sequence.
• gene_or_intergene_length – The length of the region in the target genome, indicating whether it lies within a gene or in an intergenic region.
• target_genome_gene_ratio – The ratio of genes to the total genome size in the target genome, offering insight into the genomic structure, with a higher ratio indicating a more gene-dense genome.