Frequently asked questions

Every 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.

No. It's a design and analysis tool used by developers, manufacturers, and laboratories. It doesn't generate diagnostic results for patients and is not itself an in vitro diagnostic device.

Customers use BLASTseq AI reports as supporting documentation in design and development files, verification packages, monitoring records, and LDT validation packets. As with any software used in a quality system, you remain responsible for validating the tool for your intended use and for the adequacy of your submission or validation. We provide a validation support package — see below.

Yes. A method description, versioning and change-control statement, and IQ/OQ support materials for customers whose quality systems require validation of software used in design or quality-system activities. Contact us to request the package.

Every run records the reference-database release and search date it ran against, along with your query sequences and scoring parameters. That means the analysis is reproducible and citable long after the fact — which matters whether you're documenting a continuous monitoring protocol under FDA special controls or establishing performance specifications under CLIA. See the method page for how scoring works and which requirements this supports.

You choose your retention window when you set up your account — up to 90 days on Assay Pro, up to 365 on Assay Teams. Basic runs are retained 7 days. When a run reaches the end of its window it's deleted, and its reports go with it, so export or download anything you intend to keep on file. Exported reports are self-describing: they carry the reference-database release, search date, query sequences, and scoring rationale, so they stay interpretable on your own systems indefinitely.

The tool uses NCBI database queries combined with custom AI-driven rules to:

• Detect sequence matches
• Identify mismatches and mutations
• Filter results by taxonomy
• Generate detailed reports for assay performance and inclusivity/exclusivity checks

BLASTseq AI is available as a cloud-hosted solution. This ensures fast database access, regular updates, and no local installation requirements.

While BLASTseq AI offers BLAST capabilities, it distinguishes itself by incorporating dedicated modules for primer and probe alignment, detection, inclusivity, and exclusivity. Rather than utilizing BLAST in conjunction with various sequence alignment and analysis tools, BLASTseq AI consolidates all analyses into a single, integrated platform. This streamlines the analytical process, enabling the completion of comprehensive analyses in minutes, rather than days or weeks. BLASTseq AI also generates reports to support your organization's documentation needs.

AI chat uses effort-based billing, so the credit charge varies depending on the work required for each interaction. Factors may include the selected AI model, prompt and response size, request complexity, and any tool or retrieval work performed. Structured Inclusivity/Exclusivity and Variant Analysis reports are unlocked separately for 200 credits each.

BLASTseq AI protects sensitive assay and sequence information throughout the analysis workflow. Primers, probes, query sequences, run data, analysis results, and AI chat content are protected using encryption during transmission and storage.

No. BLASTseq AI does not use your primers, probes, query sequences, analysis results, or AI chat content to train AI or large language models.

On Basic, run and analysis data is automatically deleted after 7 days. Assay Pro users can choose automatic deletion after 7, 30, or 90 days. Each Assay Teams user can choose automatic deletion after 7, 30, 90, 180, or 365 days. Users on every plan can manually delete a selected run sooner from Run History.

Yes. You can manually delete a selected run from Run History at any time. This permanently deletes the uploaded sequence, run, analysis data, and generated reports associated with that RID and cannot be undone. Export or download any report you intend to keep before deleting the run.

Yes. AI chat conversations and sessions can be manually deleted by the user from Chat History.

Currently, BLASTseq AI utilizes the NCBI GenBank database. At this time, use of other databases is available as a customized solution. Contact us for more details.

Currently analyses are generated using databases used by NCBI. We are working on including additional databases, and we'd love to hear from our users which other databases they would want made available.

Yes — result sharing is available for Assay Pro and Assay Teams users.

Yes. For more information, please contact us.

Yes — you can watch a demonstration here, or contact us to arrange a walkthrough.

Yes — paste your full panel and BLASTseq AI checks every primer and probe individually for inclusivity/exclusivity and against every other member of the panel for dimer and cross-hybridization risk. Available to Assay Pro and Assay Teams users.

You can easily input your sequences in plain text and CSV formats. We're also working to support additional formats, like FASTA, very soon.

Both DNA and RNA sequences are supported.

Results include alignment maps, mismatch summaries, inclusivity/exclusivity reporting, and detection predictions.

Yes — alignments are presented visually, base-by-base, with mismatches highlighted.

Yes. Analysis results may be exported in CSV or PDF format.

We accept major credit cards (Visa, Mastercard, American Express, Discover), PayPal, bank ACH, and wire transfers. Please note that we do not accept purchase orders.

To upgrade your account, please log in to your BLASTseq AI account, navigate to the “Billing & Subscriptions” section, and click the “Upgrade” button.

Yes, you can cancel your subscription at any time. You will continue to have access to all features and data until the end of your current billing cycle.