Your assay didn't change. The database did. BLASTseq AI runs live BLAST alignment, scores each mismatch by position and hybridization potential, checks every oligo in your panel against every other, and returns a versioned, timestamped record of inclusivity, exclusivity, and variant impact. Any target. Any assay. IVD or LDT.
How every run is documented →From sequence input to analysis reports in minutes - see the complete in silico workflow.
BLASTseq AI demo · 2 min Design. Verify. Document. In minutes, not days.
BLASTseq AI queries live NCBI databases and evaluates every hit on three dimensions: sequence identity, the way BLAST always has; mismatch location impact; and hybridization ΔG°T, the thermodynamic measure that predicts real-world binding better than percent identity alone. These resolve into a single call per hit — with the contributing factors shown, so you can explain why a hit was called non-detecting.
Evaluate every primer and probe against curated inclusivity and exclusivity sets in one pass — target strains and clades, related species, near neighbors, background flora, population variant sets, or whatever your assay has to discriminate against. Get an amplification score per target with the thermodynamic and alignment data behind it, not a hit table you have to interpret yourself.
Running more than one primer-probe set in the same reaction? BLASTseq AI checks every pair in your panel against every other for dimer formation and cross-hybridization risk — from a 4-plex qPCR to a several-hundred-amplicon NGS panel, where the pairwise combinations stop being something anyone checks by hand. It's the failure mode that shows up in the wet lab, not in a single-primer BLAST search.
Identify mutations, insertions, and deletions across matched sequences, and see which ones actually change assay performance versus which are silent. Catch the population SNP sitting under a primer binding site that causes allele dropout — and the false homozygous call that follows it — alongside the clade-associated polymorphism that quietly drops your inclusivity by two percent. Grouped by impact, so you're not scrolling a hundred near-identical rows to find the one that matters.
Every run compiles into a structured record: inclusivity and exclusivity calls, dimer and cross-hybridization risk, variant impact, the reasoning behind each score, and the reference-database release and search date the analysis ran against. Reproducible, attributable, and formatted to export straight into design and development files, a verification package, or a CLIA validation packet.
Every run delivers structured, interrogable output — from raw alignments to detection groups, inclusivity and exclusivity summaries, and variant impact. Switch samples to see the same workflow on pathogen ID, germline carrier screening, and a resistance marker.
Pathogen identification Candida auris species identification with clade-stratified inclusivity and close-Candida exclusivity.
Static preview of a species-identification run across the C. auris clades and the Candida haemulonii complex.
Alignments expose mismatch position and the contributing factors behind each explained call.
Binding locations are shown for the target and close Candida relatives, including a primer-site polymorphism with an impact call.
GCCTGTTTGAGCGTCRTTTCBindingCCTCAAATCAGGTAGGAHTACCCGCTGReviewCCTCCGCTTATTGATATGCTTABindingMatched accessions are grouped into target, near-neighbor, and further-review classes for a clear species call.
Coverage is organized by C. auris clade so meaningful sequence variation is visible instead of flattened into one percentage.
| Primary target set | Detected |
| Variant / clade set | Review |
| Related sequence set | Excluded |
A primer-site polymorphism is grouped by impact so reviewers can see which change can affect detection.
| Region | Change | Impact |
|---|---|---|
| Primer site | SNP | Review |
| Probe region | Mismatch | Silent |
| Amplicon | Indel | Impact |
Germline carrier screening Population-variation coverage across the ACMG 2023 100-variant CFTR carrier-screening context.
Static preview of an amplicon analysis framed around population variation and carrier-screening coverage.
Aligned population sequences make primer and probe binding coverage reviewable across the intended variant set.
The preview surfaces a population SNP under a primer site and shows the resulting dropout-risk assessment.
GCCTGTTTGAGCGTCRTTTCBindingCCTCAAATCAGGTAGGAHTACCCGCTGReviewCCTCCGCTTATTGATATGCTTABindingVariant-bearing sequences are grouped by expected amplification outcome, including a no-impact example for comparison.
Coverage is organized by population group to show where primer and probe design needs closer review.
| Primary target set | Detected |
| Variant / clade set | Review |
| Related sequence set | Excluded |
Variants are grouped by impact, including the primer-site SNP that can create allele dropout and an explicitly silent result.
| Region | Change | Impact |
|---|---|---|
| Primer site | SNP | Review |
| Probe region | Mismatch | Silent |
| Amplicon | Indel | Impact |
Resistance marker Candida auris FKS1 analysis showing resistant versus wild-type discrimination and homolog exclusivity.
Static preview of a resistance-marker run for C. auris, with resistant and wild-type sequence groups.
Alignments show the marker region and the mismatch factors contributing to the resistant or wild-type call.
Oligo binding is checked against the marker sequence and related gene-family homologs.
GCCTGTTTGAGCGTCRTTTCBindingCCTCAAATCAGGTAGGAHTACCCGCTGReviewCCTCCGCTTATTGATATGCTTABindingSequences are grouped into resistant-marker, wild-type, and further-review classes.
The target marker is reviewed across matched C. auris sequences while homologs are retained for exclusivity review.
| Primary target set | Detected |
| Variant / clade set | Review |
| Related sequence set | Excluded |
Marker changes are grouped by their effect on resistant versus wild-type discrimination, with the reasoning retained.
| Region | Change | Impact |
|---|---|---|
| Primer site | SNP | Review |
| Probe region | Mismatch | Silent |
| Amplicon | Indel | Impact |
Analytical specificity is a required performance characteristic for molecular assays: demonstrate the assay detects what it claims across the diversity of the target, and doesn't detect what it shouldn't. The problem is that the diversity keeps growing, and most of it never arrives as a culturable isolate, a reference material, or a characterized sample.
FDA has acknowledged this directly. In its special controls guideline for nucleic acid–based tuberculosis assays, the Agency states that in silico testing may be acceptable as an alternative for inclusivity testing for strains that are difficult to study. Across a growing set of molecular device classifications — including point-of-care and over-the-counter classifications finalized in mid-2026 — FDA writes the method into the special controls by name: a documented protocol for the continuous monitoring, identification, and handling of genetic mutations and novel isolates or strains, through regular review of published literature and periodic in silico analysis of target sequences to detect possible mismatches.
For laboratories, the same evidence sits under a different regulator. Establishing performance specifications for an LDT under CLIA requires analytical specificity, including interfering substances — and the same availability problem applies.
The logic holds outside infectious disease too. A carrier screening or oncology panel can lose an allele to a population SNP sitting under a primer binding site, and report a false homozygous result — a risk the ACMG and AMP standards for CFTR testing name explicitly. A veterinary or food-safety assay faces the same strain diversity with less reference material available. An NGS amplicon panel with four hundred primer pairs carries cross-hybridization risk no single-primer BLAST search will surface.
And it isn't a one-time exercise. Sequence databases grow continuously, and an assay evaluated against last year's database has not been evaluated against this year's. Recommended variant sets change too — ACMG replaced the 23-variant CF carrier screening panel with 100 variants in 2023, and every panel rebuilt to match needs its primer coverage rechecked. BLASTseq AI is built for the recurring version of this work: run it, score it, keep the record.
BLASTseq AI supports your analytical specificity assessment and monitoring activities; it does not discharge any regulatory obligation. In silico findings guide assay review and inform appropriate wet-lab evaluation. They do not replace laboratory validation. BLASTseq AI is not certified, approved, endorsed, or recognized by FDA, CMS, CAP, ACMG, AOAC, or any regulatory, professional, or accrediting body.
Drop in your primer, probe or amplicon sequence - or an existing assay design. No file wrangling, no setup.
BLASTseq aligns against the live NCBI database, applies taxonomy-based filtering, and groups identical hits automatically.
Inclusivity, exclusivity, and variant findings in a clean, shareable record — with the reference-database release and search date stamped in. Export it to your team, your design and development files, or your validation packet.
Skip the manual BLAST-hit spreadsheet. Inclusivity, exclusivity, and dimer checks across your whole panel in one pass.
Establishing performance specifications means documenting analytical specificity. Generate that evidence — and the record behind it — against current sequence data.
Screen hundreds of amplicons for cross-hybridization, and catch the population SNP under a primer site before it becomes a false homozygous call.
Analytical specificity evidence generated as a byproduct of the run, in a form your design and development files can hold.
One defensible method across every client assay — and a record their QA team can file without rework.
Screen assay coverage against emerging strains during active response, at response speed.
“The inclusivity screening alone saves me an entire day of work per assay. This should have existed a long time ago.”
“We needed inclusivity and exclusivity data we could put straight into our design history file. BLASTseq AI cut a two-week verification cycle down to an afternoon.”
“What I appreciated most was that it didn't just give me a score - it explained the result. That's what we actually need when writing up validation reports.”
“I've been manually interpreting BLAST results for years. BLASTseq AI gave me the same answer in under two minutes. I didn't think that was possible.”
Assay Pro and Assay Teams users choose their retention period when they set up their account — up to 90 days on Assay Pro, up to 365 on Assay Teams. Basic runs are retained 7 days. Set it once; it applies to every run.
Export or download any report you intend to keep on file. When a run reaches the end of its retention window, its reports go with it.
Reference-database release, search date, query sequences, scoring parameters, and result rationale are captured in the report itself, so it stays interpretable and reproducible on your own systems long after the run is gone.
Sequences, results, and chat content are never used to train models. Encrypted in transit and at rest.
Start free and pay as you go, or subscribe for a monthly credit allowance. Pricing is per user. AI chat credits are charged based on the effort required for each interaction, while each structured report type costs 200 credits to unlock.
🎁 20 welcome credits on signup - plus an extra 200 bonus credits on your first purchase of 20+ credits.
Everything you need to know about how BLASTseq AI fits your workflow.
Browse all FAQsEvery hit is evaluated on three dimensions: sequence identity, mismatch location impact, and hybridization ΔG°T. These resolve into a single composite call, with the contributing factors shown so you can understand the result.
BLASTseq AI is used by molecular diagnostics manufacturers, assay developers, NGS and germline panel designers, CDMOs, clinical laboratories, and public health and surveillance teams to analyze and document the analytical specificity of primer, probe, and amplicon sequences. It's a development and quality-system tool, not a diagnostic device.
Inclusivity and exclusivity analysis; cross-reactivity screening; mismatch and variant impact assessment including primer-site dropout risk; multiplex dimer and cross-hybridization checking; taxonomy-based filtering; and accession grouping — for qPCR, dPCR, isothermal, and amplicon-based NGS assays.
Both. Any assay that uses oligonucleotides to target a sequence — qPCR, dPCR, RT-PCR, isothermal amplification, amplicon-based NGS, hybrid capture, targeted enrichment. For large panels, the pairwise cross-hybridization check scales to several hundred amplicons, which is where manual review stops being feasible.
Both. For a germline assay, the inclusivity question becomes coverage across population variation, and the highest-value output is identifying population SNPs under primer or probe binding sites — the cause of allele dropout and false homozygous calls. The CFTR carrier screening sample in the output showcase demonstrates this.
Any sequence represented in the reference databases: bacterial, viral, fungal, and parasitic targets; resistance markers; human germline and somatic loci; veterinary, food-safety, and environmental targets. The method is the same regardless of what you're targeting.
Run a sample analysis — no signup required. Three pre-loaded examples: Candida auris identification, CFTR carrier screening, and an FKS1 resistance marker. Same workflow, three different assay types.