CRISPRPrep

Use Add files or drag more files into the upload area to append FASTA or JSON files from different folders. The accumulated file list can contain up to 100 files and 100 MB combined. An invalid addition keeps the files already selected. Use Reset to clear the selection. Loading an example replaces the current input after the example finishes loading.

Click Load example and choose Upload FASTA (five genomes), Paste sequence (416 sequences with Sample / Seq_Name / organism headers), NCBI accession (five IDs), or Import JSON results (five CRISPRCasFinder files). The selected data fills the corresponding input; click Run to start. FASTA and pasted examples each load about 23 MB. Detection inputs require the configured detector; JSON examples can be processed without it.

Upload or paste FASTA, or enter nucleotide accession IDs to fetch sequences from NCBI automatically. Successful sequences are combined into one FASTA with accession headers preserved and submitted to CRISPRCasFinder on the Linux server. Only retrieval progress and failed IDs are shown before the CRISPR results. After detection and CSV processing complete, use CRISPRCasFinder JSON to download result.json with the original sequence names. For imported JSON, use Download JSON before running CSV processing; saved results do not retain the uploaded JSON files. Evidence settings filter that JSON; they do not change the detector’s search parameters. Detection must be configured by the administrator.

The threshold is inclusive: 3 retains levels 3 and 4. Level 1 preserves the original script’s broad inclusion, including arrays with missing evidence levels. Higher thresholds exclude unknown levels. These are CRISPRCasFinder evidence categories, not probability scores. The default minimum of two actual Spacer regions preserves the original multi-spacer rule.

Unprocessed CSV contains Folder, Organism_Name, Seq_Name, Orientation, Spacer_Sequence and DR_Consensus after evidence and spacer-count filtering, but before normalization. Processed CSV applies the selected ND and organism-wide N filters, reverses the row order of negative arrays, and adds Reverse_Complement_Sequence, Reverse_Complement_DR and Effective_DR. Counts for removed rows may overlap between filtering rules.

Uploaded FASTA and JSON files use their filename without the final .fasta, .fna, .fa or .json extension as the sample name. All sequences in one uploaded FASTA share that sample name. NCBI sequences use the requested accession ID; aliases resolving to the same sequence use the first successfully fetched ID. Pasted FASTA requires >Sample Seq_Name Organism_Name: the first field is Sample / Folder, the second is the sequence ID, and the remaining text is the organism description. For example, >702 NZ_JOLF01000001.1 Cronobacter sakazakii strain 702 contig0001, whole genome shotgun sequence uses 702 as Sample / Folder. FASTA sequence IDs are preserved; any internal IDs needed to distinguish colliding contigs are restored to their original names in the downloaded JSON. Seq_Name follows the CRISPR array Name in that JSON. Duplicate sample and array names receive numeric suffixes; unnamed arrays get stable generated names. Organism names use the description before the first comma. Arrays from separate samples are kept separate when reordering. If an organism has an N-containing spacer after extraction, the default filter removes all extracted rows with that organism name across every input file.