LOOM CRISPR Search — Animal Reference Genomes

Reference Genomes

Select an animal host to browse CRISPR off-target matches. These reference genomes help ensure diagnostic guides don't cross-react with host DNA.

Select an animal host to view off-target matches

#	Sequence (23-mer)	Position	PAM	Matches

Select an animal host above to view off-target CRISPR matches in its genome

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Select an animal host, load its FM-index, then search any DNA sequence for off-target matches

NCBI

NCBI RefSeq Animal Genomes

Reference assemblies for key zoonotic reservoir hosts and livestock species. Used for CRISPR off-target screening.

Dataset: RefSeq Representative Genomes
Species: Bat (Rousettus), Chicken, Pig, Cow, Camel, Mouse
Accessed: March 2026
License: Public domain (US Government work)
URL: ncbi.nlm.nih.gov/datasets

Citation: Sayers EW, et al. "Database resources of the National Center for Biotechnology Information." Nucleic Acids Research, 2024, 52(D1):D33-D43.

LOOM

LOOM FM-Index Engine

The search engine powering this tool. A Burrows-Wheeler Transform (BWT) based FM-index compiled to 195 KB of WebAssembly, enabling sub-millisecond exact-match search in the browser.

Library: brenda (Rust crate)
Binary: 195 KB WASM
Method: FM-index with suffix array sampling
License: Open source

Method: Ferragina P, Manzini G. "Opportunistic data structures with applications." FOCS 2000. IEEE, 2000, pp. 390-398.

Why Animal Genomes?

When designing CRISPR diagnostics for zoonotic pathogens, guides must not cross-react with host animal DNA. For example, an Ebola diagnostic used in a bat habitat shouldn't match bat genomic sequences. This database enables that off-target screening.

Use case: Off-target validation for field diagnostics
Coverage: Key reservoir hosts for each WHO priority pathogen
Cross-reference: Use with Human Pathogens database

Off-Target Analysis Glossary

Key concepts for animal genome screening

Off-target Match

A location in a non-target genome where a CRISPR guide sequence has exact or near-exact complementarity. In diagnostic contexts, off-target matches in host animal DNA could cause false positives.

Zoonotic Reservoir

An animal species that naturally harbors a pathogen without showing disease. Examples: bats for Ebola/Nipah, camels for MERS, waterfowl for influenza A. Field diagnostics deployed in these environments must avoid host DNA cross-reactivity.

Host Specificity

The degree to which a CRISPR guide targets only the intended pathogen and not the host genome. A guide with zero off-target matches in both human and relevant animal genomes has the highest host specificity.

Cross-reactivity

When a diagnostic assay produces a signal from non-target nucleic acid. CRISPR diagnostics can cross-react if guide sequences match host DNA — this is precisely what this tool helps detect and avoid.