{"uid":"cap_QdgxYIc9rTxgqBYJEPggj","slug":"crispr-off-target-similarity-scorer-ad357447","name":"CRISPR Off-Target Similarity Scorer","description":"Compares one guide with caller-supplied candidate protospacers, weights mismatches in the guide’s final ten positions twice, applies a simple NGG PAM penalty, and ranks a transparent similarity score. It does not search a genome, model bulges, chromatin or nuclease-specific biology, and must not be used as a clinical or laboratory safety decision.","url":"https://bio.halowerk.com/v1/crispr-offtarget","method":"POST","headers":{},"bodySchema":{"type":"object","properties":{"guide":{"type":"string","pattern":"^[ACGT]+$","maxLength":30,"minLength":17,"description":"Guide sequence written 5-prime to 3-prime."},"candidates":{"type":"array","items":{"type":"object","required":["id","protospacer","pam"],"properties":{"id":{"type":"string","maxLength":128,"minLength":1},"pam":{"type":"string","pattern":"^[ACGT]+$","maxLength":8,"minLength":2},"protospacer":{"type":"string","pattern":"^[ACGT]+$","maxLength":30,"minLength":17}},"additionalProperties":false},"maxItems":1000,"minItems":1}}},"responseSchema":null,"example":null,"exampleRequest":null,"tags":["x402"],"displayCostAmount":"0.004","displayCostAsset":"USDC","priceDynamic":false,"priceHint":null,"priceStatus":"priced","priceSource":"probe","requiresHandshake":false,"reviewCount":0,"rating":{"score":"0.00","successRate":"0.00","reviews":0,"stars":null,"state":"unrated"},"availabilityStatus":"unknown","priceObserved":null,"sessionDeposit":null,"pricing":{"kind":"static","summary":"$0.004/call","primary":{"kind":"static","protocol":"x402","network":"base","amountUsd":"0.004","per":"call","confidence":"exact"},"accepted":[{"kind":"static","protocol":"x402","network":"base","amountUsd":"0.004","per":"call","confidence":"exact"}]},"paymentMethods":[{"uid":"pm_6_arF6G3vqPCd8lBohg1z","protocol":"x402","methodType":"crypto","chain":"base","mode":"charge","costAmount":"0.004","costPer":"request","priority":0,"asset":"0x833589fCD6eDb6E08f4c7C32D4f71b54bdA02913","unit":"request","depositMicros":null,"planRef":null}],"brandName":null,"brandSlug":null,"brandBaseUrl":null,"brandDocsUrl":null,"whatItDoes":"Ranks user-supplied candidate protospacers against a guide RNA sequence using a mismatch-weighted similarity score with NGG PAM penalty, emphasizing the guide's seed region (final 10 positions).","exampleAgentPrompt":"Score these 5 candidate protospacers against my guide RNA sequence ACGTACGTACGTACGTACGT for off-target similarity — their IDs are C1 through C5 with protospacers and NGG PAMs as listed — and rank them by how likely they are to be off-target sites based on seed-region mismatches.","exampleUseCases":[{"title":"Screen candidate off-target sites pre-experiment","prompt":"I have a 20-nt CRISPR guide sequence GTATCGATCGATCGATCGAT and a list of 50 genomic candidates with their protospacers and NGG PAMs — can you score and rank them by off-target similarity so I know which ones to worry about before I run my experiment?"},{"title":"Validate guide specificity for research paper","prompt":"For my manuscript I need to show my guide RNA ACGATCGATCGATCGATCGA has low off-target risk — please score these 10 candidate sequences with their PAMs against it and give me a ranked similarity table I can include."},{"title":"Triage off-target candidates from alignment hits","prompt":"I pulled 200 candidate protospacer hits from a BLAST search against my guide TTGCAACGTACGTTGCAACG, each with an ID and PAM — can you run them through the seed-region mismatch scorer and tell me which top 10 have the highest similarity scores?"}],"resultDescription":"Returns a ranked list of candidate protospacers with a transparency similarity score for each, factoring in double-weighted mismatches in the guide's final 10 positions (seed region) and an NGG PAM penalty. Does not perform genome search, model bulges, chromatin accessibility, or nuclease-specific biology.","failureModes":["Invalid DNA characters in guide or protospacer (non-ACGT) returns validation error","Guide sequence shorter than 17 or longer than 30 nt rejected","Candidate array exceeds 1000 items returns limit error","PAM shorter than 2 or longer than 8 nt rejected","Missing required fields (id, protospacer, pam) per candidate returns schema error","Mismatched protospacer length vs guide may affect score interpretation"],"whenToPreferThis":"Use this endpoint when you need a fast, transparent, rule-based off-target similarity ranking for a batch of candidate protospacers without requiring genome access or complex biological modeling. Prefer this over full off-target prediction tools (e.g. Cas-OFFinder, CRISPOR) when you already have candidate sequences from upstream alignment and need a lightweight, auditable score weighted by seed-region biology. Not suitable for clinical or laboratory safety decisions.","instructions":null,"reviewSummary":null,"reviewSummaryHighlights":null,"reviewSummaryConcerns":null,"reviewSummaryGeneratedAt":null,"activationCount":0,"lastUsedAt":null,"lastSuccessfullyRanAt":null,"lastHealthCheckAt":"2026-09-14T06:36:12.434Z","isFirstParty":false}