Sequence Search
DNA, RNA, Peptide & Protein Sequence Searches
Patent Sequence Search & Analysis
Patent sequence search and analysis
Identify relevant biological sequences across global patent literature.
IIPRD provides specialized patent sequence search and analysis services to identify and analyze nucleotide sequences (DNA and RNA) and amino acid sequences (proteins) disclosed in patent documents worldwide. By combining sequence-based searching across all major databases with in-depth patent literature analysis, we help businesses, researchers and IP professionals evaluate the patent landscape surrounding biological sequences and sequence-based inventions, and make informed decisions on patentability, competitive intelligence and freedom-to-operate.
Why patent sequence searching matters
Biological sequences sit at the heart of modern innovation in biotechnology, pharmaceuticals, diagnostics and therapeutics. A single nucleotide or amino acid sequence can appear, in identical or variant form, across thousands of patent publications and granted patents worldwide, often described in long sequence listings rather than searchable text. Conventional keyword search cannot reliably surface these disclosures.
Our approach combines sequence-based searching with patent literature analysis to identify identical, similar and potentially relevant biological sequences disclosed in patent documents. The result is a clear view of the sequence-related patent landscape that supports patentability and novelty assessments, freedom-to-operate (FTO) evaluation, competitive intelligence and portfolio decisions for sequence-based inventions.
Our patent sequence search services
Five focused services that connect your sequence of interest to the relevant patent disclosures and the decisions that depend on them.
Identify identical or similar DNA, RNA and protein sequences disclosed in global patent literature to uncover potentially relevant patent documents and biological sequence disclosures.
Identify relevant prior-art patent documents containing identical or similar sequences to support preliminary novelty and patentability assessments of biological inventions.
Identify potentially relevant patents and applications disclosing sequences of interest to support assessment of patent risks across research, development, manufacturing or commercialization.
Analyze patent documents associated with specific nucleotide or amino acid sequences to map the landscape, identify key patent holders, and evaluate technology and filing trends.
Review patent documents containing sequences of interest to assess portfolio relevance, identify overlapping disclosures, and support IP due diligence and strategic decision-making.
Each search is scoped to your sequence, technology area and objective, from a single-sequence check to large sequence listings and portfolio-scale studies.
From sequence input to analytical report
A structured, repeatable workflow that pairs rigorous sequence searching with expert patent analysis.
Sequence input and normalization
Review the provided nucleotide or amino acid sequence, sequence identifiers and relevant search parameters.
Sequence similarity searching
Search relevant patent and biological databases and sequence disclosures using suitable sequence-comparison methods and search tools.
Patent document identification
Retrieve potentially relevant patent publications, granted patents and associated sequence disclosures.
Technical and patent analysis
Evaluate sequence similarity alongside the disclosed biological function, technical context, claims and relevant patent information.
Analytical reporting
Deliver a structured report identifying relevant patent documents, sequence references, key findings and potential implications for patentability or FTO assessment.
We search all major sequence and patent databases
IIPRD runs sequence searches across the major public biological databases, dedicated patent sequence databases, and professional alignment and analysis tools, so that identical, variant and homologous sequences are captured wherever they are disclosed.
Biological sequence databases
- GenBank (NCBI)
- EMBL-ENA (EBI)
- DDBJ
- UniProt and Swiss-Prot
- RefSeq and PDB
- Non-redundant protein and nucleotide collections
Patent sequence databases
- GENESEQ and other curated patent sequence collections
- CAS and STN sequence resources
- USPTO, EPO and WIPO PatentScope sequence data
- GenBank, EMBL and DDBJ patent divisions
- Major commercial patent sequence platforms
- Global published and granted patent coverage
Alignment and analysis tools
- BLAST (blastn, blastp, tblastn, tblastx)
- Smith-Waterman local alignment
- FASTA and motif or subsequence search
- Percentage identity and coverage filtering
- Variant, degenerate and Markush handling
- Professional sequence-search platforms
Who we support
Our patent sequence search and analysis services support organizations working with biological sequences and sequence-based technologies.
Patent research expertise, applied to biological sequences
IIPRD combines patent research expertise with technical analysis to help clients navigate complex patent landscapes involving biological sequences, with actionable insight for R&D planning, prosecution support, portfolio evaluation and commercialization strategy.
Sequence and patent expertise
Life sciences specialists who read sequence disclosures and patent claims together.
All major databases
Comprehensive coverage across biological, patent and commercial sequence resources.
Rigorous alignment methods
BLAST, Smith-Waterman and motif search, tuned to the right identity and coverage.
Decision-ready reporting
Structured reports that tie sequence hits to claims, function and implications.
Global patent coverage
Searches spanning published and granted patents across jurisdictions.
Confidential handling
Sequences and objectives handled under strict confidentiality and access control.
Patent sequence search, frequently asked questions
1. What is a patent sequence search?
A patent sequence search identifies nucleotide (DNA and RNA) and amino acid (protein) sequences that are disclosed in patent publications and granted patents worldwide. Instead of relying on keywords, it compares your sequence of interest against sequence disclosures using biological alignment methods, so that identical, similar and homologous sequences are surfaced even when they are buried in long sequence listings.
2. Which types of sequences can you search?
We search nucleotide sequences (DNA and RNA) and amino acid sequences (proteins and peptides), including full-length sequences, fragments, variants and defined subsequences or motifs, depending on the objective of the search.
3. Which databases does IIPRD search?
IIPRD searches all major databases, including public biological resources such as GenBank, EMBL-ENA, DDBJ, UniProt, Swiss-Prot and RefSeq, dedicated patent sequence collections such as GENESEQ, CAS and STN resources, and patent sequence data from the USPTO, EPO, WIPO PatentScope and the GenBank, EMBL and DDBJ patent divisions, alongside major commercial patent sequence platforms.
4. How is a patent sequence search different from a text or keyword search?
Keyword search depends on how a sequence is named or described, and most sequences in patents are disclosed only in sequence listings rather than in searchable prose. A sequence search compares the actual biological sequence, so it finds relevant disclosures that keyword search would miss.
5. What search and alignment methods do you use?
We use established sequence-comparison methods and tools, including BLAST (blastn, blastp, tblastn and tblastx), Smith-Waterman local alignment, FASTA and motif or subsequence searching, with parameters chosen to suit the sequence type and the question being asked.
6. What is the difference between an identity search and a similarity or homology search?
An identity search looks for exact or near-exact matches, while a similarity or homology search also captures related sequences that differ by substitutions, insertions or deletions. We agree the percentage identity and coverage thresholds with you so that the search is neither too narrow nor too broad for the objective.
7. How does a sequence search support patentability and novelty assessment?
By identifying prior-art patent documents that disclose identical or similar sequences, the search provides the sequence-based evidence needed to support a preliminary view on the novelty and patentability of a biological invention before or during patent prosecution.
8. How does it support freedom-to-operate (FTO)?
An FTO-oriented sequence search identifies potentially relevant patents and applications that disclose sequences of interest, helping you understand possible patent risks associated with research, development, manufacturing or commercialization of a sequence-based product.
9. Can you analyze the patent landscape around a sequence or technology?
Yes. We analyze the patent documents associated with specific nucleotide or amino acid sequences to map the landscape, identify key patent holders and assignees, and evaluate technology areas and filing trends for competitive intelligence.
10. Can you handle large sequence listings or whole portfolios?
Yes. Engagements can range from a single sequence to large sequence listings and portfolio-scale studies. We agree the scope, sampling approach, deliverables and timeline based on the number of sequences and the complexity of the analysis.
11. Do you search variants, degenerate sequences and Markush structures?
Where relevant, searches can account for sequence variants, degenerate nucleotide representations and sequence-related Markush or consensus disclosures, so that functionally related sequences are considered, subject to the scope agreed for the engagement.
12. What information do you need to start a search?
Useful starting information includes the nucleotide or amino acid sequence (for example in FASTA format), any sequence identifiers or SEQ ID references, the sequence type, the relevant technology area, the intended use of the search, and any jurisdictions of interest.
13. What deliverables will I receive?
You receive a structured analytical report identifying the relevant patent documents, sequence references and alignment details, key findings, and the potential implications for patentability, FTO, landscape or portfolio decisions, scoped to the engagement.
14. How is confidentiality of my sequences protected?
Sequences, identifiers and objectives are handled within IIPRD's confidential, access-controlled environment, aligned with applicable contractual and confidentiality obligations, including non-disclosure agreements where required.
15. How long does a patent sequence search take?
Timelines depend on the number and length of sequences, the search type, the identity and coverage thresholds, and the depth of analysis. A project-specific timeline is agreed after scoping the engagement.